CParty: hierarchically constrained partition function of RNA pseudoknots.

Motivation: Biologically relevant RNA secondary structures are routinely predicted by efficient dynamic programming algorithms that minimize their free energy. Starting from such algorithms, one can devise partition function algorithms, which enable stochastic perspectives on RNA structure ensembles. As the most prominent example, McCaskill's partition function algorithm is derived from pseudoknot-free energy minimization.

Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot.

Understanding and targeting functional RNA structures towards treatment of coronavirus infection can help us to prepare for novel variants of SARS-CoV-2 (the virus causing COVID-19), and any other coronaviruses that could emerge via human-to-human transmission or potential zoonotic (inter-species) events. Leveraging the fact that all coronaviruses use a mechanism known as -1 programmed ribosomal frameshifting (-1 PRF) to replicate, we apply algorithms to predict the most energetically favourable secondary structures (each nucleotide involved in at most one pairing) that may be involved in regulating the -1 PRF event in coronaviruses, especially SARS-CoV-2. We compute previously unknown most stable structure predictions for the frameshift site of coronaviruses via hierarchical folding, a biologically motivated framework where initial non-crossing structure folds first, followed by subsequent, possibly crossing (pseudoknotted), structures.

Unveiling hidden structural patterns in the SARS-CoV-2 genome: Computational insights and comparative analysis.

SARS-CoV-2, the causative agent of COVID-19, is known to exhibit secondary structures in its 5' and 3' untranslated regions, along with the frameshifting stimulatory element situated between ORF1a and 1b. To identify additional regions containing conserved structures, we utilized a multiple sequence alignment with related coronaviruses as a starting point. We applied a computational pipeline developed for identifying non-coding RNA elements.

SparseRNAfolD: optimized sparse RNA pseudoknot-free folding with dangle consideration.

Motivation: Computational RNA secondary structure prediction by free energy minimization is indispensable for analyzing structural RNAs and their interactions. These methods find the structure with the minimum free energy (MFE) among exponentially many possible structures and have a restrictive time and space complexity ( time and space for pseudoknot-free structures) for longer RNA sequences. Furthermore, accurate free energy calculations, including dangle contributions can be difficult and costly to implement, particularly when optimizing for time and space requirements.

Prediction of Alzheimer's in People with Coronavirus Using Machine Learning.

Background: One of the negative effects of the COVID-19 illness, which has affected people all across the world, is Alzheimer's disease. Oblivion after COVID-19 has created a variety of issues for many people. Predicting this issue in COVID-19 patients can considerably lessen the severity of the problem.

Morphological and Molecular Characterization of sp. n. (Dorylaimida, Qudsianematidae) from Iran.

A new species of the genus , recovered from the northwest of Iran, was described based on morphological, morphometric, and molecular data. eshtiaghii sp. n.

Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.

Multiple coronaviruses including MERS-CoV causing Middle East Respiratory Syndrome, SARS-CoV causing SARS, and SARS-CoV-2 causing COVID-19, use a mechanism known as -1 programmed ribosomal frameshifting (-1 PRF) to replicate. SARS-CoV-2 possesses a unique RNA pseudoknotted structure that stimulates -1 PRF. Targeting -1 PRF in SARS-CoV-2 to impair viral replication can improve patients' prognoses.

Regulatory effect of sericin protein in inflammatory pathways; A comprehensive review.

Sericin protein is a type of protein derived from silk cocoons. Sericin hydrogen bonds cause adhesion to the silk cocoon. This substance contains a large amount of serine amino acids in its structure.

Pseudoknots in RNA Structure Prediction.

RNA molecules play active roles in the cell and are important for numerous applications in biotechnology and medicine. The function of an RNA molecule stems from its structure. RNA structure determination is time consuming, challenging, and expensive using experimental methods.

Factors affecting hospital services overutilization and reductive strategies in Iran: a qualitative study to explore experts' views.

Objectives: This study aimed to investigate the viewpoints of the main stakeholders of the Iranian healthcare system about the overutilization of hospital services and strategies to eliminate or reduce it in Iran.

Methods: This is a qualitative study and thematic data analysis using face-to-face semi-structured interviews and Focus Group Discussions (FGDs). We conducted eight interviewers and two FGDs with hospital stakeholders including faculty members, insurance organizations' authorities, experienced hospital administrative staff, hospital managers, and health-care providers.

Strategies for utilisation management of hospital services: a systematic review of interventions.

Background: To achieve efficiency and high quality in health systems, the appropriate use of hospital services is essential. We identified the initiatives intended to manage adult hospital services and reduce unnecessary hospital use among the general adult population.

Methods: We systematically reviewed studies published in English using five databases (PubMed, ProQuest, Scopus, Web of Science, and MEDLINE via Ovid).

KnotAli: informed energy minimization through the use of evolutionary information.

Background: Improving the prediction of structures, especially those containing pseudoknots (structures with crossing base pairs) is an ongoing challenge. Homology-based methods utilize structural similarities within a family to predict the structure. However, their prediction is limited to the consensus structure, and by the quality of the alignment.

Supervised promoter recognition: a benchmark framework.

Motivation: Deep learning has become a prevalent method in identifying genomic regulatory sequences such as promoters. In a number of recent papers, the performance of deep learning models has continually been reported as an improvement over alternatives for sequence-based promoter recognition. However, the performance improvements in these models do not account for the different datasets that models are evaluated on.

Quality of life and asthma control in pregnant women with asthma.

Background: Asthma is the most commonly occurring respiratory illness during pregnancy. Associations with complications of pregnancy and adverse perinatal outcome have been established. However, little is known about quality of life (QoL) in pregnant women with asthma and how it relates to asthma control particularly for Iran.

In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells.

Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis.

New insights into the identity of Das, Khan and Loof, 1969 (Dorylaimida) as derived from its morphological and molecular characterization, with the proposal of its transference to Andrássy, 2002.

Three Iranian populations of are studied, including their morphological and morphometric characterization, molecular analysis (LSU-rDNA) and the description of the male for the first time. For comparative purposes, this species is distinguished by its 1.10 to 1.

3D-Printing Replication of Porous Media for Lab-Scale Characterization Research.

Simplifying fluid-flow physics in conventional reservoirs is convenient by assuming uniform lithology and system-geometry with minimal rock/hydrocarbon interactions. Such simplification restrains mathematical models' ability to simulate unconventional reservoirs' actual flow behavior and production performance. Researchers can achieve precise adaption for the physics of fluid flow in porous media if they geometrically characterize the system under study appropriately, and there are minimal interactions indeed.

Morphological and molecular characterization of n. sp. and additional data on (Altherr, 1950) Altherr, 1952 (Dorylaimida: Nordiidae) from northwest of Iran.

Two species of the genus , one new and one known, collected in natural vegetation and cultivated soils in northwest of Iran, are studied. n. sp.

Description of a new dagger nematode, n. sp. (Nematoda: Longidoridae) and additional data on the three known species of the genus from northwest of Iran.

n. sp. collected from the rhizosphere of common wheat ( L.

Regulation of von Willebrand Factor Gene in Endothelial Cells That Are Programmed to Pluripotency and Differentiated Back to Endothelial Cells.

Endothelial cells play a central role in physiological function and pathophysiology of blood vessels in health and disease. However, the molecular mechanism that establishes the endothelial phenotype, and contributes to its signature cell type-specific gene expression, is not yet understood. We studied the regulation of a highly endothelial-specific gene, von Willebrand factor (VWF), in induced pluripotent stem cells generated from primary endothelial cells (human umbilical vein endothelial cells [HUVEC] into a pluripotent state [HiPS]) and subsequently differentiated back into endothelial cells.

Organizing palliative care in the rural areas of Iran: are family physician-based approaches suitable?

Introduction: The provision of palliative end-of-life care (P/EOLc) for patients, wherever they live, is an increasingly important service, particularly given the increasing rates of cancer and other life-threatening diseases in Iran. However, unfortunately, those living in the rural areas of Iran are greatly disadvantaged with respect to this type of care. Therefore, the present study explored the feasibility of organizing P/EOLc in the rural areas of Iran.