Soundness of Unravelings for Conditional Term Rewriting Systems via Ultra-Properties Related to Linearity

Unravelings are transformations from a conditional term rewriting system (CTRS, for short) over an original signature into an unconditional term rewriting systems (TRS, for short) over an extended signature. They are not sound w.r.t. reduction for every CTRS, while they are complete w.r.t. reduction. Here, soundness w.r.t. reduction means that every reduction sequence of the corresponding unraveled TRS, of which the initial and end terms are over the original signature, can be simulated by the reduction of the original CTRS. In this paper, we show that an optimized variant of Ohlebusch's unraveling for a deterministic CTRS is sound w.r.t. reduction if the corresponding unraveled TRS is left-linear or both right-linear and non-erasing. We also show that soundness of the variant implies that of Ohlebusch's unraveling. Finally, we show that soundness of Ohlebusch's unraveling is the weakest in soundness of the other unravelings and a transformation, proposed by Serbanuta and Rosu, for (normal) deterministic CTRSs, i.e., soundness of them respectively implies that of Ohlebusch's unraveling.Comment: 49 pages, 1 table, publication in Special Issue: Selected papers of the "22nd International Conference on Rewriting Techniques and Applications (RTA'11)

Evidence-based approach to thrombophilia testing

Thrombophilia can be identified in about half of all patients presenting with VTE. Testing has increased tremendously for various indications, but whether the results of such tests help in the clinical management of patients has not been settled. I use evidence from observational studies to conclude that testing for hereditary thrombophilia generally does not alter the clinical management of patients with VTE, with occasional exceptions for women at fertile age. Because testing for thrombophilia only serves limited purpose this should not be performed on a routine basis

A Reduction-Preserving Completion for Proving Confluence of Non-Terminating Term Rewriting Systems

We give a method to prove confluence of term rewriting systems that contain non-terminating rewrite rules such as commutativity and associativity. Usually, confluence of term rewriting systems containing such rules is proved by treating them as equational term rewriting systems and considering E-critical pairs and/or termination modulo E. In contrast, our method is based solely on usual critical pairs and it also (partially) works even if the system is not terminating modulo E. We first present confluence criteria for term rewriting systems whose rewrite rules can be partitioned into a terminating part and a possibly non-terminating part. We then give a reduction-preserving completion procedure so that the applicability of the criteria is enhanced. In contrast to the well-known Knuth-Bendix completion procedure which preserves the equivalence relation of the system, our completion procedure preserves the reduction relation of the system, by which confluence of the original system is inferred from that of the completed system

Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph

Using EpiLymph case-control data, we found that chronic lymphocytic leukemia patients were more likely to have abnormal reactive serological patterns to Epstein Barr virus than controls. Here, we aimed to assess whether this association is modified by genetic variants. We examined 1,305 Single Nucleotide Polymorphisms from 300 selected genes related to various pathways in 240 cases and 513 controls from five European centers. In a recessive model, patients positive to aberrant antibody pattern and homozygous for rare genotypes in rs8113877T>G or rs17576A>G of the MMP9 gene were at highest risk of chronic lymphocytic leukemia. In a dominant model, TP73 showed the highest risk in patients positive to aberrant antibody pattern and homozygous for the wild-type genotype in rs1885859G>C or rs3765701A>T. All interactions were additive and no main effect was observed. The strong interactions observed may be indicative of a specific pathway in cancer genesis. Confirmation of these results is warranted

Bacterial flagellar motors and osmoelectric molecular rotation by an axially transmembrane well and turnstile mechanism

AbstractBacterial ion-driven flagellar motors are the smallest known rotatory mechanical devices, natural or artificial, their overall diameter being only about 25 nm or one millionth of an inch. They are unique in the fields of biology and engineering. This paper develops a possible osmoelectric or local electrokinetic mechanism of molecular rotatory motion in bilayer membranes, which may help to explain how bacterial flagellar motors work, and may incidentally encourage new developments in the bioenergetics and biomechanics of enzyme, osmoenzyme and porter action

Epstein-Barr Virus Latency in B Cells Leads to Epigenetic Repression and CpG Methylation of the Tumour Suppressor Gene Bim

In human B cells infected with Epstein-Barr virus (EBV), latency-associated virus gene products inhibit expression of the proapoptotic Bcl-2-family member Bim and enhance cell survival. This involves the activities of the EBV nuclear proteins EBNA3A and EBNA3C and appears to be predominantly directed at regulating Bim mRNA synthesis, although post-transcriptional regulation of Bim has been reported. Here we show that protein and RNA stability make little or no contribution to the EBV-associated repression of Bim in latently infected B cells. However, treatment of cells with inhibitors of histone deacetylase (HDAC) and DNA methyltransferase (DNMT) enzymes indicated that epigenetic mechanisms are involved in the down-regulation of Bim. This was initially confirmed by chromatin immunoprecipitation analysis of histone acetylation levels on the Bim promoter. Consistent with this, methylation-specific PCR (MSP) and bisulphite sequencing of regions within the large CpG island located at the 59 end of Bim revealed significant methylation of CpG dinucleotides in all EBV-positive, but not EBV-negative B cells examined. Genomic DNA samples exhibiting methylation of the Bim promoter included extracts from a series of explanted EBV-positive Burkitt’s lymphoma (BL) biopsies. Subsequent analyses of the histone modification H3K27-Me3 (trimethylation of histone H3 lysine 27) and CpG methylation at loci throughout the Bim promoter suggest that in EBV-positive B cells repression of Bim is initially associated with this repressive epigenetic histone mark gradually followed by DNA methylation at CpG dinucleotides. We conclude that latent EBV initiates a chain of events that leads to epigenetic repression of the tumour suppressor gene Bim in infected B cells and their progeny. This reprogramming of B cells could have important implications for our understanding of EBV persistence and the pathogenesis of EBV-associated disease, in particular BL

Atrial fibrillation detection using insertable cardiac monitor after stroke: a real-word cohort study

First published: 09 November 2022Objective: This study aimed to report the real‐world atrial fibrillation (AF) diagnostic yield of the implantable cardiac monitor (ICM) in patients with stroke or transient ischemic attack (TIA), and compare it to patients with an ICM for unexplained syncope. Methods: We used patient data from device clinics across the United States of America with ICM remote monitoring via PaceMate™, implanted for stroke or TIA, and unexplained syncope. Patients with known AF or atrial flutter were excluded. The outcome was AF lasting ≥2 min, adjudicated by International Board of Heart Rhythm Examiners certified cardiac device specialists. Results: We included a total of 2469 patients, 51.1% with stroke or TIA (mean age: 69.7 [SD: 12.2] years, 41.1% female) and 48.9% with syncope (mean age: 67.0 [SD: 17.1] years, 59.4% female). The cumulative AF detection rate in patients with stroke or TIA was 5.5%, 8.9%, and 14.0% at 12, 24, and 36 months, respectively. The median episode duration was 73 (interquartile range: 10–456) min, ranging from 2 min to 40.9 days, with 52.3%, 28.6%, and 4.4% of episodes lasting at least 1, 6, and 24 h, respectively. AF detection was increased by age (adjusted hazard ratio [for every 1‐year increase]: 1.024, 95% confidence interval: 1.008–1.040; p = .003), but was not influenced by sex (p = .089). For comparison, the cumulative detection rate at 12, 24, and 36 months were, respectively, 2.4%, 5.2%, and 7.4% in patients with syncope. Conclusion: Patients with stroke or TIA have a higher rate of AF detection. However, this real‐world study shows significantly lower AF detection rates than what has been previously reported.Jean J. Noubiap, Gijo Thomas, Melissa E. Middeldorp, John L. Fitzgerald, Curtis Harper, Prashanthan Sander

Sequence variation of Epstein-Barr virus: viral types, geography, codon usage and diseases

138 new Epstein-Barr virus (EBV) genome sequences have been determined. 125 of these and 116 from previous reports were combined to produce a multiple sequence alignment of 241 EBV genomes, which we have used to analyze variation within the viral genome. The type 1/type2 classification of EBV remains the major form of variation and is defined mostly by EBNA2 and EBNA3, but the type 2 SNPs at the EBNA3 locus extend into the adjacent gp350 and gp42 genes, whose products mediate infection of B cells by EBV. A small insertion within the BART miRNA region of the genome was present in 21 EBV strains. EBV from saliva of USA patients with chronic active EBV infection aligned with the wild type EBV genome, with no evidence of WZhet rearrangements. The V3 polymorphism in the Zp promoter for BZLF1 was found to be frequent in nasopharyngeal carcinoma cases both from Hong Kong and Indonesia. Codon usage was found to differ between latent and lytic cycle EBV genes and the main forms of variation of the EBNA1 protein have been identified.IMPORTANCE Epstein-Barr virus causes most cases of infectious mononucleosis and post-transplant lymphoproliferative disease. It contributes to several types of cancer including Hodgkin's lymphoma, Burkitt's lymphoma, diffuse large B cell lymphoma, nasopharyngeal carcinoma and gastric carcinoma. EBV genome variation is important because some of the diseases associated with EBV have very different incidences in different populations and geographic regions - differences in the EBV genome might contribute to these diseases. Some specific EBV genome alterations that appear to be significant in EBV associated cancers are already known and current efforts to make an EBV vaccine and antiviral drugs should also take account of sequence differences in the proteins used as targets

Assessment of available online educational resources for patients with atrial fibrillation

Background: A diagnosis of atrial fibrillation (AF) often leads patients to search online for information, which can expose them to information of varied quality. Objective: We conducted a qualitative systematic review of websites that contain useful information regarding AF. Methods: The following terms were searched on 3 search engines (Google/Yahoo/Bing): (Atrial fibrillation for patients), (What is atrial fibrillation), (Atrial fibrillation patient information), (Atrial fibrillation educational resources). Inclusion criteria included websites with comprehensive AF information and information about treatment options. The Patient Education Materials Assessment Tool for Printable Materials (PEMAT-P) and PEMAT for Audiovisual Materials assessed understandability and actionability (score range 0–100). Those with a mean PEMAT-P score of .70, meaning acceptable understandability and actionability, underwent DISCERN score assessment of information content quality and reliability (score range 16–80). Results: The search yielded 720 websites that underwent full review. After exclusions, 49 underwent full scoring. The mean overall PEMAT-P score was 69.3 6 17.2. The mean PEMAT-AV score was 63.4 6 13.6. Of the websites that scored .70% on the PEMAT-P, 23 (46%) underwent DISCERN scoring. The mean DISCERN score was 54.7 6 4.6. Conclusions: There is a wide variation in the understandably, actionability, and quality of websites, many not providing patientlevel materials. Knowledge of quality websites could provide an important adjunct for improving patients understanding of AF.Melissa E. Middeldorp, Ellen Lyrtzis, Kyle Heath, Tanya Hall, Kadhim Kadhim, Prashanthan Sander

Sex disparities in enrolment and reporting of outcomes by sex in contemporary clinical trials of atrial fibrillation

Background:Underrepresentation of females in randomized controlled trials (RCTs)limits generalizability and quality of the evidence guiding treatment of females. This study aimed to measure the sex disparities in participants' recruitment in RCTs of atrial fibrillation (AF) and determine associated factors, and to describe the frequency of outcomes reported by sex. Methods:MEDLINE was searched to identify RCTs of AF published between January 1, 2011, and November 20, 2021, in 12 top‐tier journals. We measured the enrollment of females using the enrollment disparity difference (EDD) which is the difference between the proportion of females in the trial and the proportion of females with AF in the underlying general population (obtained from the Global Burden of Disease). Random‐effects meta‐analyses of the EDD were performed, and multivariable meta‐regression was used to explore factors associated with disparity estimates. We also determined the proportion of trials that included sex‐stratified results. Results:Out of 1133 records screened, 142 trials were included, reporting on a total of 133 532 participants. The random‐effects summary EDD was−0.125 (95%confidence interval [CI] =−0.143 to−0.108), indicating that females were under‐enrolled by 12.5 percentage points. Female enrollment was higher in trials with higher sample size (750, adjusted odds ratio [aOR] 1.065, 95% CI:1.008–1.125), higher mean participants' age (aOR: 1.006, 95% CI: 1.002–1.009), and lower in trials conducted in North America compared to Europe (aOR: 0.945, 95% CI:0.898–0.995). Only 36 trials (25.4%) reported outcomes by sex, and of these 29(80.6%) performed statistical testing of the sex‐by‐treatment interaction. Conclusion:Females remain substantially less represented in RCTs of AF, and sex‐stratified reporting of primary outcomes is infrequent. These findings call for urgent action to improve sex equity in enrollment and sex‐stratified outcomes' reporting in RCTs of AF.Jean Jacques Noubiap, Gijo Thomas, Ulrich Flore Nyaga, John L. Fitzgerald, Celine Gallagher, Melissa E. Middeldorp, Prashanthan Sander