Clinical relevance of expanded quantitative urine culture in health and disease.

"Expanded quantitative urine culture (EQUC)" is an enhanced culture protocol for the detection of viable microbes in urine specimens. Using a large volume of urine and different sets of cultural conditions, EQUC is able to uncover a wide range of bacteria and fungi (yeasts) that were otherwise undetected by the standard urinary culture. In addition to common urinary pathogens, EQUC has been shown to detect emerging and new pathogens, and commensal microbiota. Although the usefulness of EQUC protocol in clinical set up has not yet been fully established, recent studies have demonstrated that EQUC can provide valuable information regarding symptom resolution, treatment responses and diagnosis of major urinary disorders including urinary tract infections, urinary incontinence and other lower urinary tract symptoms. EQUC may also help in evaluating the utility of beneficial microbiota as biotherapeutics. This narrative minireview describes the current research findings regarding the clinical utility of EQUC in characterizing the role of urinary microbiome and uropathogens in health and disease. The literature which are written in English, available on "PubMed" and contain any of the terms- "expanded quantitative urine culture", "enhanced quantitative urine culture" and "EQUC" in the abstracts were used as the source articles to prepare this minireview.

RNAMotifComp: a comprehensive method to analyze and identify structurally similar RNA motif families.

MOTIVATION: The 3D structures of RNA play a critical role in understanding their functionalities. There exist several computational methods to study RNA 3D structures by identifying structural motifs and categorizing them into several motif families based on their structures. Although the number of such motif families is not limited, a few of them are well-studied. Out of these structural motif families, there exist several families that are visually similar or very close in structure, even with different base interactions. Alternatively, some motif families share a set of base interactions but maintain variation in their 3D formations. These similarities among different motif families, if known, can provide a better insight into the RNA 3D structural motifs as well as their characteristic functions in cell biology. RESULTS: In this work, we proposed a method, RNAMotifComp, that analyzes the instances of well-known structural motif families and establishes a relational graph among them. We also have designed a method to visualize the relational graph where the families are shown as nodes and their similarity information is represented as edges. We validated our discovered correlations of the motif families using RNAMotifContrast. Additionally, we used a basic Naïve Bayes classifier to show the importance of RNAMotifComp. The relational analysis explains the functional analogies of divergent motif families and illustrates the situations where the motifs of disparate families are predicted to be of the same family. AVAILABILITY AND IMPLEMENTATION: Source code publicly available at https://github.com/ucfcbb/RNAMotifFamilySimilarity.

A Case Report of Moyamoya Disease Presenting as Recurrent Right-Sided Weakness.

Moyamoya disease is a cerebrovascular condition characterized by progressive occlusion of the cerebral vessels, particularly in the circle of Willis. This report describes the case of a 12-year-old boy presenting with a history of recurrent right-sided weakness over a period of seven years. Magnetic resonance imaging revealed evidence of both old and recent infarcts, as well as encephalomalacic changes. The diagnosis was confirmed by magnetic resonance angiography, which demonstrated severe stenosis in both internal carotid arteries and the presence of significant collateral formation. In Bangladesh, surgical revascularization for Moyamoya disease had not been previously attempted, and due to financial constraints, the patient's family opted for conservative management with anti-platelet therapy and regular follow-ups. Although a hereditary component is often presumed in Moyamoya disease, no such familial history was identified in this case. Additionally, no associations with immunological, infectious, hematological, vascular, or congenital syndromes were found. Mortality rates for Moyamoya disease are approximately 10% in adults and 4.3% in children, with a significant proportion of affected individuals experiencing cognitive decline. However, the patient in this case maintained intact cognitive function, and with diligent follow-up and anticoagulation therapy, it was anticipated that his functional capacity would remain stable.

RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis.

The significance of RNA functions and their role in evolution and disease control have remarkably increased the research scope in the field of RNA science. Though the availability of RNA structure data in PBD has been growing tremendously, maintaining their quality and integrity has become the greater challenge. Since the data available in PDB are results of different independent research, they might contain redundancy. As a result, there remains a possibility of data bias for both protein and RNA chains. Quite a few studies have been conducted to remove the redundancy of protein structures by introducing high-quality representatives. However, the amount of research done to remove the redundancy of RNA structures is still very low. To remove RNA chain redundancy in PDB, we have introduced RNA-NRD, a non-redundant dataset of RNA chains based on sequence and 3D structural similarity. We compared RNA-NRD with the existing non-redundant RNA structure dataset RS-RNA and showed that it has better-formed clusters of redundant RNA chains with lower average RMSD and higher average PSI, thus improving the overall quality of the dataset.

LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.

A fast-growing number of non-coding RNA structures have been resolved and deposited in Protein Data Bank (PDB). In contrast to the wide range of global alignment and motif search tools, there is still a lack of local alignment tools. Among all the global alignment tools for RNA 3D structures, STAR3D has become a valuable tool for its unprecedented speed and accuracy. STAR3D compares the 3D structures of RNA molecules using consecutive base-pairs (stacks) as anchors and generates an optimal global alignment. In this article, we developed a local RNA 3D structural alignment tool, named LocalSTAR3D, which was extended from STAR3D and designed to report multiple local alignments between two RNAs. The benchmarking results show that LocalSTAR3D has better accuracy and coverage than other local alignment tools. Furthermore, the utility of this tool has been demonstrated by rediscovering kink-turn motif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.

Inflammation-Induced Adverse Pregnancy and Neonatal Outcomes Can Be Improved by the Immunomodulatory Peptide Exendin-4.

Preterm birth is the leading cause of neonatal morbidity and mortality worldwide. Inflammation is causally linked to preterm birth; therefore, finding an intervention that dampens maternal and fetal inflammatory responses may provide a new strategy to prevent adverse pregnancy and neonatal outcomes. Using animal models of systemic maternal inflammation [intraperitoneal injection of lipopolysaccharide (LPS)] and fetal inflammation (intra-amniotic administration of LPS), we found that (1) systemic inflammation induced adverse pregnancy and neonatal outcomes by causing a severe maternal cytokine storm and a mild fetal cytokine response; (2) fetal inflammation induced adverse pregnancy and neonatal outcomes by causing a mild maternal cytokine response and a severe fetal cytokine storm; (3) exendin-4 (Ex4) treatment of dams with systemic inflammation or fetal inflammation improved adverse pregnancy outcomes by modestly reducing the rate of preterm birth; (4) Ex4 treatment of dams with systemic, but not local, inflammation considerably improved neonatal outcomes, and such neonates continued to thrive; (5) systemic inflammation facilitated the diffusion of Ex4 through the uterus and the maternal-fetal interface; (6) neonates born to Ex4-treated dams with systemic inflammation displayed a similar cytokine profile to healthy control neonates; and (7) treatment with Ex4 had immunomodulatory effects by inducing an M2 macrophage polarization and increasing anti-inflammatory neutrophils, as well as suppressing the expansion of CD8+ regulatory T cells, in neonates born to dams with systemic inflammation. Collectively, these results provide evidence that dampening maternal systemic inflammation through novel interventions, such as Ex4, can improve the quality of life for neonates born to women with this clinical condition.