Blessed Virgin Mary – a sign of hope in Roman liturgy

Među naslovima kojima Crkva u liturgiji časti Blaženu Djevicu Mariju nalaze se i nazivi koji Mariju oslovljavaju kao znak, zoru i majku nade. U glavnom dijelu članka autor propitkuje primjenu tih naziva u euharistijskim slavljima i u molitvi Časoslova, konkretno u Gospinim blagdanima Bezgrješnoga začeća, Marijina rođenja i uznesenja, Marije Kraljice, zajedničkim slavljima Blažene Djevice Marije i molitvi Zdravo Kraljice. Kratak tumač objašnjava liturgijsku upotrebu tih naziva i u Zbirci misa o Blaženoj Djevici Mariji i u slavljima sv. Marije u subotu. U zaključku se naglašava činjenica kako novo usmjerenje crkvenog učenja o Isusovoj majci odlučno utječe na oblikovanje liturgijskih tekstova za marijanska spomenslavlja dajući im kristološko i ekleziološko usmjerenje.Among the titles with which the Church praises the Blessed Virgin Mary in Roman liturgy are also the appellations of Mary such as a sign of hope, the dawn of hope and the mother of hope. In the main part, the author discusses the use of these names in Eucharistic celebrations and in the Divine Office, precisely in the Feasts of the Immaculate Conception, the Marian Birth and Assumption, Queen Mary and in the common celebrations of the Blessed Virgin Mary as well as in the Prayer Salve Regina. A brief display and interpretation explain the liturgical use of these names in the collection of Masses of the Blessed Virgin Mary and in the celebration of St. Mary on Saturday. The conclusion underlines the fact that a new orientation of the Church’s teachings about Jesus’ Mother decisively influences the formulation and proposal of liturgical texts for the Marian celebrations, giving them a Christological and Ecclesiological character

A gene pattern mining algorithm using interchangeable gene sets for prokaryotes

<p>Abstract</p> <p>Background</p> <p>Mining gene patterns that are common to multiple genomes is an important biological problem, which can lead us to novel biological insights. When family classification of genes is available, this problem is similar to the pattern mining problem in the data mining community. However, when family classification information is not available, mining gene patterns is a challenging problem. There are several well developed algorithms for predicting gene patterns in a pair of genomes, such as FISH and DAGchainer. These algorithms use the optimization problem formulation which is solved using the dynamic programming technique. Unfortunately, extending these algorithms to multiple genome cases is not trivial due to the rapid increase in time and space complexity.</p> <p>Results</p> <p>In this paper, we propose a novel algorithm for mining gene patterns in more than two prokaryote genomes using interchangeable sets. The basic idea is to extend the pattern mining technique from the data mining community to handle the situation where family classification information is not available using interchangeable sets. In an experiment with four newly sequenced genomes (where the gene annotation is unavailable), we show that the gene pattern can capture important biological information. To examine the effectiveness of gene patterns further, we propose an ortholog prediction method based on our gene pattern mining algorithm and compare our method to the bi-directional best hit (BBH) technique in terms of COG orthologous gene classification information. The experiment show that our algorithm achieves a 3% increase in recall compared to BBH without sacrificing the precision of ortholog detection.</p> <p>Conclusion</p> <p>The discovered gene patterns can be used for the detecting of ortholog and genes that collaborate for a common biological function.</p

Germline DDX41 mutations cause ineffective hematopoiesis and myelodysplasia

DDX41 mutations are the most common germline alterations in adult myelodysplastic syndromes (MDSs). The majority of affected individuals harbor germline monoallelic frameshift DDX41 mutations and subsequently acquire somatic mutations in their other DDX41 allele, typically missense R525H. Hematopoietic progenitor cells (HPCs) with biallelic frameshift and R525H mutations undergo cell cycle arrest and apoptosis, causing bone marrow failure in mice. Mechanistically, DDX41 is essential for small nucleolar RNA (snoRNA) processing, ribosome assembly, and protein synthesis. Although monoallelic DDX41 mutations do not affect hematopoiesis in young mice, a subset of aged mice develops features of MDS. Biallelic mutations in DDX41 are observed at a low frequency in non-dominant hematopoietic stem cell clones in bone marrow (BM) from individuals with MDS. Mice chimeric for monoallelic DDX41 mutant BM cells and a minor population of biallelic mutant BM cells develop hematopoietic defects at a younger age, suggesting that biallelic DDX41 mutant cells are disease modifying in the context of monoallelic DDX41 mutant BM

Determination of Risk Factors for Predicting Bladder-Urethra Injury in Cases of Pelvic Bone Fracture: A Retrospective Single Center Study

Purpose Pelvis fractures are associated with bladder and urethral injury (BUI). The purpose of this study was to identify risk factors associated with BUI in patients with pelvic fracture. Methods Patients (> 18 years) with pelvic injury (N = 314) at our hospital between January 2015 and June 2020 were retrospectively analyzed for age, sex, cause of injury, initial vital signs, urine red blood cell (RBC) count, Glasgow Coma Scale and Abbreviated Injury Scale score, Injury Severity Score, preperitoneal pelvic packing, and femur, lumbar spine, and pelvic fractures. Results Compared with the BUI-absent group, the BUI-present group had a greater percentage of patients who were male (79.2% vs. 55.9%; p = 0.026), had a urine RBC count/high power field (HPF) ≥ 30 (94.4% vs. 38.8%; p < 0.001), underwent preperitoneal pelvic packing (37.5% vs. 18.6%; p = 0.035), had symphysis pubis diastasis (33.3% vs. 11.7%; p = 0.008), and had sacroiliac joint dislocation (54.2% vs. 23.4%; p = 0.001). Independent risk factors associated with BUI were symphysis pubis diastasis [odds ratio (OR) was 3.958 (95% confidence interval: 1.191–13.154); p = 0.025] and a urine RBC count/HPF ≥ 30 [OR = 25.415 (95% confidence interval: 3.252–198.637); p = 0.006]. Of those with BUI, 15 patients were diagnosed at the trauma bay, and 9 had a delayed diagnosis. Conclusion Patients with pelvic injury who display symphysis pubis diastasis or have a urine RBC count/HPF ≥ 30 are at higher risk of BUI, therefore, further BUI investigations should be considered

Determination of risk factors associated with surgical site infection in patients undergoing preperitoneal pelvic packing for unstable pelvic fracture

Background Several recent studies have shown that preperitoneal pelvic packing (PPP) effectively produces hemostasis in patients with unstable pelvic fractures. However, few studies have examined the rate of surgical site infections (SSIs) in patients undergoing PPP following an unstable pelvic fracture. The purpose of the present study was to evaluate factors associated with SSI in such patients. Methods We retrospectively reviewed the medical charts of 188 patients who developed hemorrhagic shock due to pelvic fracture between April 2012 and May 2021. Forty-four patients were enrolled in this study. Results SSI occurred in 15 of 44 patients (34.1%). The SSIs occurred more frequently in cases of repacking during the second-look surgery (0 vs. 4 [26.7%], P=0.010) and combined bladder-urethra injury (1 [3.4%] vs. 4 [26.7%], P=0.039). The incidence of SSIs was not significantly different between patients undergoing depacking within or after 48 hours (12 [41.4%] vs. 5 [33.3%], P=0.603). The mean time to diagnosis of SSI was 8.1±3.9 days from PPP. The most isolated organism was Staphylococcus epidermidis. Conclusions Repacking and combined bladder-urethra injury are potential risk factors for SSI in patients with unstable pelvic fracture. Close observation is recommended for up to 8 days in patients with these risk factors. Further, 48 hours after PPP, removing the packed gauze on cessation of bleeding and not performing repacking can help prevent SSI. Additional analyses are necessary with a larger number of patients with the potential risk factors identified in this study

ComPath: comparative enzyme analysis and annotation in pathway/subsystem contexts

<p>Abstract</p> <p>Background</p> <p>Once a new genome is sequenced, one of the important questions is to determine the presence and absence of biological pathways. Analysis of biological pathways in a genome is a complicated task since a number of biological entities are involved in pathways and biological pathways in different organisms are not identical. Computational pathway identification and analysis thus involves a number of computational tools and databases and typically done in comparison with pathways in other organisms. This computational requirement is much beyond the capability of biologists, so information systems for reconstructing, annotating, and analyzing biological pathways are much needed. We introduce a new comparative pathway analysis workbench, ComPath, which integrates various resources and computational tools using an interactive spreadsheet-style web interface for reliable pathway analyses.</p> <p>Results</p> <p>ComPath allows users to compare biological pathways in multiple genomes using a spreadsheet style web interface where various sequence-based analysis can be performed either to compare enzymes (e.g. sequence clustering) and pathways (e.g. pathway hole identification), to search a genome for <it>de novo </it>prediction of enzymes, or to annotate a genome in comparison with reference genomes of choice. To fill in pathway holes or make <it>de novo </it>enzyme predictions, multiple computational methods such as FASTA, Whole-HMM, CSR-HMM (a method of our own introduced in this paper), and PDB-domain search are integrated in ComPath. Our experiments show that FASTA and CSR-HMM search methods generally outperform Whole-HMM and PDB-domain search methods in terms of sensitivity, but FASTA search performs poorly in terms of specificity, detecting more false positive as E-value cutoff increases. Overall, CSR-HMM search method performs best in terms of both sensitivity and specificity. Gene neighborhood and pathway neighborhood (global network) visualization tools can be used to get context information that is complementary to conventional KEGG map representation.</p> <p>Conclusion</p> <p>ComPath is an interactive workbench for pathway reconstruction, annotation, and analysis where experts can perform various sequence, domain, context analysis, using an intuitive and interactive spreadsheet-style interface. </p

A molecular basis for neurofibroma-associated skeletal manifestations in NF1

Purpose: Plexiform neurofibromas (pNF) develop in children with neurofibromatosis type 1 (NF1) and can be associated with several skeletal comorbidities. Preclinical mouse studies revealed Nf1 deficiency in osteoprogenitor cells disrupts, in a MEK-dependent manner, pyrophosphate (PPi) homeostasis and skeletal mineralization. The etiology of NF-associated skeletal manifestations remains unknown. Methods: We used mouse models of NF1 neurofibromas to assess bone mineralization of skeletal structures adjacent to tumors. Expression of genes involved in pyrophosphate homeostasis was assessed in mouse and human NF tumors and Schwann cell cultures. We used dual-energy X-ray absorptiometry (DXA) to assess tumor-associated changes in bone mineral density (BMD) in an individual with NF1 following treatment with the MEK inhibitor selumetinib. Results: We detected increased nonmineralized bone surfaces adjacent to tumors in mouse models of NF1 neurofibromas. Expression of Enpp1, a PPi-generating ectophosphatase, and ANKH, a PPi transporter, was increased in mouse and human neurofibroma-derived tissues and Schwann cells, respectively. In one patient, tumor-associated reductions in BMD were partially rescued following therapy with selumetinib. Conclusion: Results indicate that NF-associated skeletal pathologies in NF1 are associated with dysregulated pyrophosphate homeostasis in adjacent NF tumors and suggest that treatment of NFs with MEK inhibitors may improve skeletal manifestations of the disease

iGEAK: an interactive gene expression analysis kit for seamless workflow using the R/shiny platform

Abstract Background The use of microarrays and RNA-seq technologies is ubiquitous for transcriptome analyses in modern biology. With proper analysis tools, the differential gene expression analysis process can be significantly accelerated. Many open-source programs provide cutting-edge techniques, but these often require programming skills and lack intuitive and interactive or graphical user interfaces. To avoid bottlenecks impeding seamless analysis processing, we have developed an Interactive Gene Expression Analysis Kit, we term iGEAK, focusing on usability and interactivity. iGEAK is designed to be a simple, intuitive, light-weight that contrasts with heavy-duty programs. Results iGEAK is an R/Shiny-based client-side desktop application, providing an interactive gene expression data analysis pipeline for microarray and RNA-seq data. Gene expression data can be intuitively explored using a seamless analysis pipeline consisting of sample selection, differentially expressed gene prediction, protein-protein interaction, and gene set enrichment analyses. For each analysis step, users can easily alter parameters to mine more relevant biological information. Conclusion iGEAK is the outcome of close collaboration with wet-bench biologists who are eager to easily explore, mine, and analyze new or public microarray and RNA-seq data. We designed iGEAK as a gene expression analysis pipeline tool to provide essential analysis steps and a user-friendly interactive graphical user interface. iGEAK enables users without programing knowledge to comfortably perform differential gene expression predictions and downstream analyses. iGEAK packages, manuals, tutorials, sample datasets are available at the iGEAK project homepage (https://sites.google.com/view/iGEAK)