Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of tryptophan halogenases in sponges of the genus Aplysina

ABSTRACT Marine sponges are a prolific source of novel enzymes with promising biotechnological potential. Especially halogenases, which are key enzymes in the biosynthesis of brominated and chlorinated secondary metabolites, possess interesting properties towards the production of pharmaceuticals that are often halogenated. In this study we used a polymerase chain reaction (PCR)-based screening to simultaneously examine and compare the richness and diversity of putative tryptophan halogenase protein sequences and bacterial community structures of six Aplysina species from the Mediterranean and Caribbean seas. At the phylum level, bacterial community composition was similar amongst all investigated species and predominated by Actinobacteria, Chloroflexi, Cyanobacteria, Gemmatimonadetes, and Proteobacteria. We detected four phylogenetically diverse clades of putative tryptophan halogenase protein sequences, which were only distantly related to previously reported halogenases. The Mediterranean species Aplysina aerophoba harbored unique halogenase sequences, of which the most predominant was related to a sponge-associated Psychrobacter-derived sequence. In contrast, the Caribbean species shared numerous novel halogenase sequence variants and exhibited a highly similar bacterial community composition at the operational taxonomic unit (OTU) level. Correlations of relative abundances of halogenases with those of bacterial taxa suggest that prominent sponge symbiotic bacteria, including Chloroflexi and Actinobacteria, are putative producers of the detected enzymes and may thus contribute to the chemical defense of their host.
Exercise duRing Active Surveillance for prostatE cancer—the ERASE trial: a study protocol of a phase II randomised controlled trial

Introduction Active surveillance (AS) is the preferred primary treatment strategy for men with low-risk clinically localised prostate cancer (PCa); however, the majority of these men still receive radical treatment within 10 years due to disease progression and/or fear of cancer progression. Interventions designed to suppress tumour growth, mitigate fear of cancer progression and precondition men for impending radical treatments are an unmet clinical need. Exercise has been shown to delay the progression of prostate tumours in animal models, improve physical and functional health and manage psychological outcomes in cancer patients; however, these outcomes have not been demonstrated in PCa patients undergoing AS. Methods and analysis This phase II randomised controlled trial will randomise 66 men undergoing AS to either an exercise group or a usual care group. The exercise group will perform a 12-week, supervised, high-intensity interval training programme, consisting of 3 sessions/week for 28–40 min/session. The primary outcome will be cardiorespiratory fitness. Secondary outcomes will include immunosurveillance and cancer-related biomarkers, psychosocial outcomes including fear of cancer progression and quality of life and physical function. Exploratory outcomes will include clinical indicators of disease progression. The trial has 80% power to detect a significant between-group difference in VO2peak of 3.5 mL/kg/min with a two-tailed alpha level <0.05 and a 10% dropout rate. Ethics and dissemination The study has received full ethical approval from the Health Research Ethics Board of Alberta – Cancer Committee (Protocol Number: HREBA.CC-17–0248). The findings of the study will be disseminated through public and scientific channels. Trial registration number NCT03203460; Pre-results.
Risk-Based Newborn Drug Testing in a Setting With a Low Prevalence of Maternal Drug Use.

OBJECTIVES Our objective in this study was to determine the predictive value of an institutional risk-based newborn drug-testing tool for detecting maternal drug use during pregnancy. METHODS For 5.5 months, the umbilical cords of all newborns born at the study institution were collected and analyzed at a national reference laboratory. In the context of usual clinical care, the decision to perform newborn drug testing is based on an institutional risk assessment tool. For the cohort without clinical indication for testing, cords were deidentified during the study period. Chart review was not performed. Study data were compared with a national data set during the same time period and to previous institutional data. RESULTS We tested 857 newborns, 257 of which had 1 or more identified risk factors. There were no drugs or drug metabolites that were significantly more common in the cohort without risk factors than in the clinical cohort. Alprazolam, methamphetamine, hydrocodone, and oxycodone were all significantly more commonly found in the risk-identified cohort. Amphetamine, methamphetamine, and cocaine were not detected in umbilical cords from any of the 600 newborns that would not have been identified for testing. Tetrahydrocannabinol (1.0%; n = 6) was the only illegal substance in the institution's state that would not have been detected. CONCLUSIONS Performing universal newborn drug testing in the study population would have identified an additional 6 newborns who were exposed prenatally to tetrahydrocannabinol out of 600 who were additionally tested. In areas with a low prevalence of maternal drug use, universal testing may not be cost-effective.
From general base to general acid catalysis in a sodium-specific DNAzyme by a guanine-to-adenine mutation

Abstract Recently, a few Na+-specific RNA-cleaving DNAzymes were reported, where nucleobases are likely to play critical roles in catalysis. The NaA43 and NaH1 DNAzymes share the same 16-nt Na+-binding motif, but differ in one or two nucleotides in a small catalytic loop. Nevertheless, they display an opposite pH-dependency, implicating distinct catalytic mechanisms. In this work, rational mutation studies locate a catalytic adenine residue, A22, in NaH1, while previous studies found a guanine (G23) to be important for the catalysis of NaA43. Mutation with pKa-perturbed analogs, such as 2-aminopurine (∼3.8), 2,6-diaminopurine (∼5.6) and hypoxanthine (∼8.7) affected the overall reaction rate. Therefore, we propose that the N1 position of G23 (pKa ∼6.6) in NaA43 functions as a general base, while that of A22 (pKa ∼6.3) in NaH1 as a general acid. Further experiments with base analogs and a phosphorothioate-modified substrate suggest that the exocyclic amine in A22 and both of the non-bridging oxygens at the scissile phosphate are important for catalysis for NaH1. This is an interesting example where single point mutations can change the mechanism of cleavage from general base to general acid, and it can also explain this Na+-dependent DNAzyme scaffold being sensitive to a broad range of metal ions and molecules.
Metal‐dependent assembly of a protein nano‐cage

Short, alpha‐helical coiled coils provide a simple, modular method to direct the assembly of proteins into higher order structures. We previously demonstrated that by genetically fusing de novo–designed coiled coils of the appropriate oligomerization state to a natural trimeric protein, we could direct the assembly of this protein into various geometrical cages. Here, we have extended this approach by appending a coiled coil designed to trimerize in response to binding divalent transition metal ions and thereby achieve metal ion‐dependent assembly of a tetrahedral protein cage. Ni2+, Co2+, Cu2+, and Zn2+ ions were evaluated, with Ni2+ proving the most effective at mediating protein assembly. Characterization of the assembled protein indicated that the metal ion–protein complex formed discrete globular structures of the diameter expected for a complex containing 12 copies of the protein monomer. Protein assembly could be reversed by removing metal ions with ethylenediaminetetraacetic acid or under mildly acidic conditions.
A Stochastic Model Underlying the Chain-Ladder Technique

ABSTRACT This paper presents a statistical model underlying the chain-ladder technique. This is related to other statistical approaches to the chain-ladder technique which have been presented previously. The statistical model is cast in the form of a generalised linear model, and a quasi-likelihood approach is used. It is shown that this enables the method to process negative incremental claims. It is suggested that the chain-ladder technique represents a very narrow view of the possible range of models.
Microglial ROCK is essential for chronic methylmercury‐induced neurodegeneration

Methylmercury (MeHg), an environmental pollutant, causes serious damage to many organs. Effects on the CNS were initially thought to arise from MeHg acting directly on neurons, but it also has significant effects on non‐neuronal cells such as microglia. Microglia, which are very sensitive to changes in the brain environment, show various phenotypes. We previously reported that upon short exposure to MeHg (MeHgshort) at low concentration, microglia exhibited a neuroprotective phenotype; whereas, long‐term exposure (MeHglong) induced a neurotoxic phenotype of microglia. However, contributions of microglia to MeHg‐induced CNS damage remain unknown. Even at very low concentrations, MeHglong but not MeHgshort caused significant neuronal damage associated with an increased number of reactive microglia in cortical slices from wild‐type (WT) mice. Two‐photon imaging of cortical slices from Iba1‐GFP mice revealed that microglia in control conditions exhibited elongated and complex processes with high motility. MeHglong caused a significant reduction in process motility, retraction of processes, and hypertrophic cell bodies, indicating activated microglia. Moreover, MeHglong ‐treated microglia upregulated pro‐inflammatory molecues, suggesting a change into a neurotoxic phenotype of microglia. As a molecular target, Rho‐kinase (ROCK) was found to be key for controlling microglial reactivity and neurotoxicity. Expression level of ROCK was increased by MeHglong in WT slices, which was abolished by minocycline or Y‐27632. We confirmed that MeHg directly activates microglial ROCK pathways prepared from WT mice. In addition, MeHg‐evoked damage of primary neurons was significantly enhanced by the presence of microglia from WT mice, but offset by minocycline or Y‐27632. Taken together, our data demonstrate that MeHg causes neurodegeneration by inducing a neurotoxic microglia phenotype via a ROCK‐mediated mechanism.
A meta-analysis

Background:Mediterranean dietary pattern has attracted great attention in terms of its effect on human health. However, whether Mediterranean dietary pattern is an independent protective factor for prostate cancer remains controversial. Our goal was to evaluate this association by conducting a meta-analysis of observational studies. Methods: We searched the PubMed and EMBASE database through February 2019 for relevant studies that examined the association betweenMediterranean Diet and prostate cancer risk. The combined risk estimates were computed using a DerSimonian random-effects model. Results:A total of 10 eligible studies were included in this meta-analysis. The pooled risk estimates and 95% confidence interval (CI) in relation to Mediterranean diet pattern were 0.95 (95% CI: 0.90 to 1.01) for total prostate cancer, 0.93 (95% CI: 0.75 to 1.14) for advanced prostate cancer, 0.96 (95%CI: 0.81 to 1.14) for localized prostate cancer, and 0.92 (95%CI: 0.76 to 1.11) for fatal prostate cancer. There was no evidence of heterogeneity for total (P= .326, I=12.7%), localized (P= .706, I=0.0%) and fatal prostate cancer (P= .282, I=13.0%), but not for advanced prostate cancer (P= .018, I=63.4%). Conclusion:This large meta-analysis of observational studies suggests that Mediterranean dietary pattern has no relationship with prostate cancer risk. Abbreviations: CI = confidence interval, HR = hazard ratio, MD = Mediterranean diet, OR = odds ratio, RR = relative risk.
Mir526b and Mir655 Promote Tumour Associated Angiogenesis and Lymphangiogenesis in Breast Cancer

MicroRNAs (miRNAs) are small endogenously produced RNAs, which regulate growth and development, and oncogenic miRNA regulate tumor growth and metastasis. Tumour-associated angiogenesis and lymphangiogenesis are processes involving the release of growth factors from tumour cells into the microenvioronemnt to communicate with endothelial cells to induce vascular propagation. Here, we examined the roles of cyclo-oxygenase (COX)-2 induced miR526b and miR655 in tumour-associated angiogenesis and lymphangiogenesis. Ectopic overexpression of miR526b and miR655 in poorly metastatic estrogen receptor (ER) positive MCF7 breast cancer cells resulted in upregulation of angiogenesis and lymphangiogenesis markers vascular endothelial growth factor A (VEGFA); VEGFC; VEGFD; COX-2; lymphatic vessel endothelial hyaluronan receptor-1 (LYVE1); and receptors VEGFR1, VEGFR2, and EP4. Further, miRNA-high cell free conditioned media promoted migration and tube formation by human umbilical vein endothelial cells (HUVECs), and upregulated VEGFR1, VEGFR2, and EP4 expression, showing paracrine stimulation of miRNA in the tumor microenvironment. The miRNA-induced migration and tube formation phenotypes were abrogated with EP4 antagonist or PI3K/Akt inhibitor treatments, confirming the involvement of the EP4 and PI3K/Akt pathway. Tumour supressor gene PTEN was found to be downregulated in miRNA high cells, confirming that it is a target of both miRNAs. PTEN inhibits hypoxia-inducible factor-1 (HIF1α) and the PI3K/Akt pathway, and loss of regulation of these pathways through PTEN results in upregulation of VEGF expression. Moreover, in breast tumors, angiogenesis marker VEGFA and lymphangiogenesis marker VEGFD expression was found to be significantly higher compared with non-adjacent control, and expression of miR526b and miR655 was positively correlated with VEGFA, VEGFC, VEGFD, CD31, and LYVE1 expression in breast tumour samples. These findings further strengthen the role of miRNAs as breast cancer biomarkers and EP4 as a potential therapeutic target to abrogate miRNA-induced angiogenesis and lymphangiogenesis in breast cancer.
ATP-dependent helicase activity is dispensable for the physiological functions of Recql4

Rothmund-Thomson syndrome (RTS) is a rare autosomal recessive disorder characterized by skin rash (poikiloderma), skeletal dysplasia, small stature, juvenile cataracts, sparse or absent hair, and predisposition to specific malignancies such as osteosarcoma and hematological neoplasms. RTS is caused by germ-line mutations in RECQL4, a RecQ helicase family member. In vitro studies have identified functions for the ATP-dependent helicase of RECQL4. However, its specific role in vivo remains unclear. To determine the physiological requirement and the biological functions of Recql4 helicase activity, we generated mice with an ATP-binding-deficient knock-in mutation (Recql4K525A). Recql4K525A/K525A mice were strikingly normal in terms of embryonic development, body weight, hematopoiesis, B and T cell development, and physiological DNA damage repair. However, mice bearing two distinct truncating mutations Recql4G522Efs and Recql4R347*, that abolished not only the helicase but also the C-terminal domain, developed a profound bone marrow failure and decrease in survival similar to a Recql4 null allele. These results demonstrate that the ATP-dependent helicase activity of Recql4 is not essential for its physiological functions and that other domains might contribute to this phenotype. Future studies need to be performed to elucidate the complex interactions of RECQL4 domains and its contribution to the development of RTS.
Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-Infection Estimation towards Enhanced Vaccine Efficacy Assessment

Knowledge of the time of HIV-1 infection and the multiplicity of viruses that establish HIV-1 infection is crucial for the in-depth analysis of clinical prevention efficacy trial outcomes. Better estimation methods would improve the ability to characterize immunological and genetic sequence correlates of efficacy within preventive efficacy trials of HIV-1 vaccines and monoclonal antibodies. We developed new methods for infection timing and multiplicity estimation using maximum likelihood estimators that shift and scale (calibrate) estimates by fitting true infection times and founder virus multiplicities to a linear regression model with independent variables defined by data on HIV-1 sequences, viral load, diagnostics, and sequence alignment statistics. Using Poisson models of measured mutation counts and phylogenetic trees, we analyzed longitudinal HIV-1 sequence data together with diagnostic and viral load data from the RV217 and CAPRISA 002 acute HIV-1 infection cohort studies. We used leave-one-out cross validation to evaluate the prediction error of these calibrated estimators versus that of existing estimators and found that both infection time and founder multiplicity can be estimated with improved accuracy and precision by calibration. Calibration considerably improved all estimators of time since HIV-1 infection, in terms of reducing bias to near zero and reducing root mean squared error (RMSE) to 5–10 days for sequences collected 1–2 months after infection. The calibration of multiplicity assessments yielded strong improvements with accurate predictions (ROC-AUC above 0.85) in all cases. These results have not yet been validated on external data, and the best-fitting models are likely to be less robust than simpler models to variation in sequencing conditions. For all evaluated models, these results demonstrate the value of calibration for improved estimation of founder multiplicity and of time since HIV-1 infection.
"Evaluation of the introduction of a dental virtual simulator on the performance of undergraduate dental students in the pre-clinical operative dentistry course".

INTRODUCTION Virtual reality-based platforms are becoming increasingly popular in education. The aim of this study was to evaluate the performance of undergraduate dental students with the introduction of the Moog Simodont dental trainer (VR) within the pre-clinical curriculum in the direct restorations module of the operative dentistry course using manual and digital methods. METHODS Thirty-two randomly selected year 2 undergraduate students were divided into two groups: group 1, exposed to the Moog Simodont dental trainer (VR) and group 2, no exposure to VR. All students were then evaluated in carrying out a Class I preparation in a single-blinded fashion. All preparations were evaluated by 3 assessors using a traditional manual approach and a digital software. Statistical analysis of the data was performed using chi-square test (alpha = 0.05). RESULTS The number of students who performed satisfactory preparations was more in group 1 (12/16), compared to group 2 (7/16). The percentage of satisfactory domains was significantly higher in group 1, compared to group 2, both in the manual evaluation (83.9% (94/112) and 59.8% (67/112) in group 1 and 2 respectively) and digital evaluation (85.7% (96/112) and 55.4% (62/112) in group 1 and 2 respectively) (p < 0.05). There was no significant difference between the manual and digital methods of evaluation with regards to the percentage of satisfactory or unsatisfactory preparations (p > 0.05). CONCLUSIONS The use of the Moog Simodont dental trainer (VR) significantly improved the satisfactory performance of students. The virtual reality simulator may be a valuable adjunct in the undergraduate direct restorations course and for student remedials. This article is protected by copyright. All rights reserved.
Smoking-Related DNA Methylation is Associated with DNA Methylation Phenotypic Age Acceleration: The Veterans Affairs Normative Aging Study

DNA methylation may play a critical role in aging and age-related diseases. DNA methylation phenotypic age (DNAmPhenoAge) is a new aging biomarker and predictor of chronic disease risk. While smoking is a strong risk factor for chronic diseases and influences methylation, its influence on DNAmPhenoAge is unknown. We investigated associations of self-reported and epigenetic smoking indicators with DNAmPhenoAge acceleration in a longitudinal aging study in eastern Massachusetts. DNA methylation was measured in whole blood samples from multiple visits for 692 male participants in the Veterans Affairs Normative Aging Study during 1999–2013. Acceleration was defined using residuals from linear regression of the DNAmPhenoAge on the chronological age. Cumulative smoking (pack-years) was significantly associated with DNAmPhenoAge acceleration, whereas self-reported smoking status was not. We observed significant validated associations between smoking-related loci and DNAmPhenoAge acceleration for 52 CpG sites, where 18 were hypomethylated and 34 were hypermethylated, mapped to 16 genes. The AHRR gene had the most loci (N = 8) among the 16 genes. We generated a smoking aging index based on these 52 loci, which showed positive significant associations with DNAmPhenoAge acceleration. These epigenetic biomarkers may help to predict age-related risks driven by smoking.
Evidence on the direct correlation between miR‐31 and IL‐22 axis in IMQ‐induced psoriasis

Psoriatic skin is characterized by a deregulated profile of miRNAs that are contributing in disease development. In this study, we focus on miR‐31, one of the upregulated miRNAs known to promote keratinocytes proliferation and migration. Moreover, miR‐31 expression induction was dependent on a large panel of cytokines including IL‐22. Here, we aimed at investigating the relationship between miR‐31‐5p and IL‐22 axis; and by searching novel molecular target for miR‐31‐5p in keratinocytes. Our data identify a direct correlation between miR‐31‐5p and IL‐22 in psoriasis with Pwp1 as new potential target. These findings confirm the important role of miR‐31 in psoriasis onset and provide a basis for further investigations in miRNAs field in context of skin diseases.
Spontaneous self-assembly and structure of perfluoroalkylalkane surfactant hemimicelles by molecular dynamics simulations

Significance Semifluorinated alkanes surfactants spontaneously form nanostructured Langmuir films at the surface of water, consisting of highly organized arrays of hemimicelles. These supramolecular nanostructures are potential candidates for numerous applications, from smart materials to medical devices. Despite all efforts, the principles governing the formation and structure of these hemimicelles are not understood. Atomistic molecular-dynamics (MD) simulations show the spontaneous formation of such aggregates strikingly resembling those experimentally observed, supporting a rational explanation for the formation, size and shape of the hemimicelles. The simulated grazing incidence X-ray diffraction spectrum matches that obtained experimentally, fully validating the MD results. Given the simplicity of these “primitive” amphiphiles compared with the common hydrophilic/hydrophobic surfactants, these results can contribute to understand self-assembly processes in general. Fully atomistic molecular-dynamics (MD) simulations of perfluoroalkylalkane molecules at the surface of water show the spontaneous formation of aggregates whose size and topography closely resemble the experimentally observed hemimicelles for this system. Furthermore, the grazing incidence X-ray diffraction (GIXD) pattern calculated from the simulation trajectories reproduces the experimental GIXD spectra previously obtained, fully validating the MD simulation results. The detailed analysis of the internal structure of the aggregates obtained by the MD simulations supports a definite rational explanation for the spontaneous formation, stability, size, and shape of perfluoroalkylalkane hemimicelles at the surface of water.