The association of subacute thyroiditis with viral diseases: a comprehensive review of literature

Introduction: Subacute thyroiditis (SAT), also known as de Quatrain's thyroiditis or granulomatous thyroiditis, is an inflammatory disease of the thyroid. Most of the time, it manifests in the thirties to fifties and is more common in women. SAT can have either viral or post-viral origin. Some viruses, like influenza, COVID-19, Epstein-Barr virus, cytomegalovirus, hepatitis, coxsackievirus 16, and mumps virus, have been linked to SAT development. The COVID-19 pandemic has affected people's lives all around the world and has changed our attitude toward the treatment of many diseases. It has also made us look deeper into the subject in a way that we would be able to treat this sort of disease with a newer insight. Objective: Regarding the importance of this issue, we decided to summarize our extensive searches from online databases, including PubMed, Google Scholar, Medline, Web of Science, and Scopus until February 2023, which we found effective in elucidating the association of subacute thyroiditis and viral diseases. Method: Different online databases were searched for narrative review articles, systemic review articles, and original articles, which were published until February 2023. Result: According to the included studies, we found that there is a correlation between SAT and several viruses such as Epstein-Barr virus, influenza virus, human immunodeficiency virus, cytomegalovirus, oral and cervical virus, hepatitis, dengue virus, and SARS-COV-2. The effect of each of the viral diseases mentioned in the SAT is given in the text. Conclusions: According to the results mentioned in the text, because SAT may be challenging for early diagnosis, due to the potential of classic symptoms as well as the interference of similar clinical symptoms between thyrotoxicosis and viral reactions, the correlation between SAT and viral diseases should be considered so that we can avoid misdiagnosis and lateness.

Transformer-based de novo peptide sequencing for data-independent acquisition mass spectrometry.

Tandem mass spectrometry (MS/MS) stands as the predominant high-throughput technique for comprehensively analyzing protein content within biological samples. This methodology is a cornerstone driving the advancement of proteomics. In recent years, substantial strides have been made in Data-Independent Acquisition (DIA) strategies, facilitating impartial and non-targeted fragmentation of precursor ions. The DIA-generated MS/MS spectra present a formidable obstacle due to their inherent high multiplexing nature. Each spectrum encapsulates fragmented product ions originating from multiple precursor peptides. This intricacy poses a particularly acute challenge in de novo peptide/protein sequencing, where current methods are ill-equipped to address the multiplexing conundrum. In this paper, we introduce Transformer-DIA, a deep-learning model based on transformer architecture. It deciphers peptide sequences from DIA mass spectrometry data. Our results show significant improvements over existing STOA methods, including DeepNovo-DIA and PepNet. Transformer-DIA enhances precision by 15.14% to 34.8%, recall by 11.62% to 31.94% at the amino acid level, and boosts precision by 59% to 81.36% at the peptide level. Integrating DIA data and our Transformer-DIA model holds considerable promise to uncover novel peptides and more comprehensive profiling of biological samples. Transformer-DIA is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/Transformer-DIA.

Transformer-based de novo peptide sequencing for data-independent acquisition mass spectrometry.

Tandem mass spectrometry (MS/MS) stands as the predominant high-throughput technique for comprehensively analyzing protein content within biological samples. This methodology is a cornerstone driving the advancement of proteomics. In recent years, substantial strides have been made in Data-Independent Acquisition (DIA) strategies, facilitating impartial and non-targeted fragmentation of precursor ions. The DIA-generated MS/MS spectra present a formidable obstacle due to their inherent high multiplexing nature. Each spectrum encapsulates fragmented product ions originating from multiple precursor peptides. This intricacy poses a particularly acute challenge in de novo peptide/protein sequencing, where current methods are ill-equipped to address the multiplexing conundrum. In this paper, we introduce Casanovo-DIA, a deep-learning model based on transformer architecture. It deciphers peptide sequences from DIA mass spectrometry data. Our results show significant improvements over existing STOA methods, including DeepNovo-DIA and PepNet. Casanovo-DIA enhances precision by 15.14% to 34.8%, recall by 11.62% to 31.94% at the amino acid level, and boosts precision by 59% to 81.36% at the peptide level. Integrating DIA data and our Casanovo-DIA model holds considerable promise to uncover novel peptides and more comprehensive profiling of biological samples. Casanovo-DIA is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/Casanovo-DIA.

Saffron and Sleep Quality: A Systematic Review of Randomized Controlled Trials.

Background: Sleep quality is defined as an individual's consent to sleep experience. Poor sleep quality has important adverse health outcomes. There are drugs to treat sleep disorders but consumption of these drugs is accompanied by adverse effects whereas herbal treatments have fewer side effects. Saffron is spice obtained from Crocus sativus flower. Several articles have been done on its effects on the quality of sleep and its safety. This review for the first time critically evaluates effect of saffron on sleep quality improvement. Method: The search technique aims to get all related published data-based up to 2022 articles. PubMed, Central, Google Scholar, and Scopus were examined. Only full reports were evaluated (abstracts were excluded). The first screening was done by title and abstract. Then full text of articles was read and irrelevant articles were removed. Duplicate articles were also removed by Endnote. By using Cochrane risk of bias tool assessment, a quality score based on probability of bias was given. Methodological characteristics were also evaluated using the criteria of Stevinson and Ernst. Result: In the systematic review, 5 randomized clinical trials with 379 participants from 3 countries were identified. In placebo-comparison trials, saffron contains a large treatment. Conclusion: It seems that saffron has a beneficial influence on duration and quality of sleep. Saffron, crocin, and safranal induce hypnotic effects by increasing the duration of sleep. Research conducted so far provides initial support and safety for use of saffron to improve sleep quality.

Detection of Methicillin-Resistant Coagulase-Negative Staphylococci and Surveillance of Antibacterial Resistance in a Multi-Center Study from Iran.

BACKGROUND: Coagulase-negative staphylococci (CNS) are a common cause of nosocomial infections. In recent years, an increase in the incidence of methicillin-resistant coagulase-negative staphylococci (MRCNS) has led to the severity of the disease. OBJECTIVES: The aim of this study was to isolate and identify MRCNS strains by oxacillin disk agar diffusion, oxacillin agar screening, and polymerase chain reaction (PCR) and to evaluate their antibacterial resistance patterns. PATIENTS AND METHODS: Totally, 122 CNS isolates were collected from the clinical specimens of four hospitals in Iran. Susceptibility testing was performed by disk agar diffusion against 15 antimicrobial agents. Then, disk agar diffusion, agar screening, and PCR were applied to determine susceptibility to oxacillin. RESULTS: Out of the 122 isolates, 92 isolates were found to be MRCNS by PCR. The sensitivities and specificities of disk agar diffusion and agar screening were 89.2% and 69% and 93.8% and 96.3%, respectively. Also, 93 CNS isolates were resistant to Methicillin according to disk agar diffusion. DISCUSSION: Our results indicated that agar screening was superior to oxacillin disk agar diffusion. A comparison between the antibiotic sensitivity patterns of the MRCNS and the Methicillin-Susceptible Coagulase-Negative Staphylococci (MSCNS) showed that the MRCNS were predominantly multiple-drug resistant isolates as the simultaneous resistance rate to 4 or more antibiotics in the MRCNS and MSCNS was 93% and 56%, respectively.