Miracle-dz/UniFAR-FTUs huggingface dataset:
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

The composition of the human microbiota is recognized as an important factor in human health and disease. Many of our cohabitating microbes belong to phylum-level divisions for which there are no cultivated representatives and are only represented by small subunit rRNA sequences. For one such taxon (SR1), which includes bacteria with elevated abundance in periodontitis, we provide a single-cell genome sequence from a healthy oral sample. SR1 bacteria use a unique genetic code. In-frame TGA (opal) codons are found in most genes (85%), often at loci normally encoding conserved glycine residues. UGA appears not to function as a stop codon and is in equilibrium with the canonical GGN glycine codons, displaying strain-specific variation across the human population. SR1 encodes a divergent tRNAGlyUCA with an opal-decoding anticodon. SR1 glycyl-tRNA synthetase acylates tRNAGlyUCA with glycine in vitro with similar activity compared with normal tRNAGlyUCC. Coexpression of SR1 glycyl-tRNA synthetase and tRNAGlyUCA in Escherichia coli yields significant β-galactosidase activity in vivo from a lacZ gene containing an in-frame TGA codon. Comparative genomic analysis with Human Microbiome Project data revealed that the human body harbors a striking diversity of SR1 bacteria. This is a surprising finding because SR1 is most closely related to bacteria that live in anoxic and thermal environments. Some of these bacteria share common genetic and metabolic features with SR1, including UGA to glycine reassignment and an archaeal-type ribulose-1,5-bisphosphate carboxylase (RubisCO) involved in AMP recycling. UGA codon reassignment renders SR1 genes untranslatable by other bacteria, which impacts horizontal gene transfer within the human microbiota.
Etude rétrospective de l'influence des polymorphismes génétiques de CYP3A4, CYP3A5 et ABCB1 des donneurs et des receveurs sur les effets des immunosuppresseurs en transplantation hépatique

La transplantation hepatique est une technique chirurgicale maitrisee, mais le devenir a long terme du greffon et de l’hote doit encore etre ameliore. L’etude pharmacogenetique des inhibiteurs de la calcineurine (CNI) devrait permettre de comprendre la variabilite de leurs effets therapeutiques et toxiques. Dans un premier temps, nous avons realise une revue de la litterature concernant la pharmacogenetique des CNI en greffe d’organe et surtout hepatique en particulier les trois polymorphismes les plus impliques dans la pharmacocinetique des CNI (CYP3A4*22, CYP3A5*3 et ABCB1 exons 12, 21, 26) et leurs eventuelles associations avec le devenir clinique du patient. L’etat actuel des connaissances valide l’interet du genotype CYP3A5*3 pour adapter au mieux la posologie precoce de tacrolimus seulement en greffe renale. Dans un second temps, nous avons mene une etude de cohorte retrospective visant a etudier la pertinence et l’interet des genotypes du donneur et du receveur d’organe mentionnes precedemment, intervenant dans le metabolisme (CYP3A4*22, CYP3A5*3) et le transport membranaire (ABCB1 exons 12, 21 et 26) de la cyclosporine et du tacrolimus en transplantation hepatique. 170 patients avec un suivi de plus de 10 ans en moyenne ont ete inclus. Les principaux resultats montrent que : l’allele CYP3A5 *1 du receveur etait associe significativement a un risque plus eleve de perte de greffon a long terme compare a l’allele CYP3A5 *3 ; l’allele TT de l’exon 12 d’ABCB1 du receveur etait associe a un risque moins eleve de rejet chronique ; et l’exposition a des doses elevees de CNI, la valeur initiale de la fonction renale et l’âge du receveur etaient egalement independamment associes au risque d’alteration de la fonction renale. La caracterisation de ces marqueurs pharmacogenetiques en transplantation hepatique pourrait permettre d’adapter les traitements immunosuppresseurs pour chaque patient transplante. D’autres voies de recherche (pharmacogenetique de la voie calcineurine, biomarqueurs precoces des lesions du greffon, .) seront necessaires pour identifier un profil personnalise pour chaque greffe afin d’adapter au mieux la strategie therapeutique a long terme.
Modulation of B-cell exosome proteins by gamma herpesvirus infection

Significance Exosomes are released from tumor cells at high levels, and multiple studies have determined that the secreted exosomes enter recipient cells and can affect their biologic and biochemical properties. In this study, the specific effects of the oncogenic herpesviruses, EBV and Kaposi sarcoma-associated virus, on the proteomes of B-cell exosomes were determined using global quantitative proteomics. The data indicate that the viruses greatly impact the protein content of exosomes with common and distinct changes induced by both viruses. It is likely that these alterations in exosome content modulate the tumor environment, potentially to enhance viral infection and promote tumorigenesis. The human gamma herpesviruses, Kaposi sarcoma-associated virus (KSHV) and EBV, are associated with multiple cancers. Recent evidence suggests that EBV and possibly other viruses can manipulate the tumor microenvironment through the secretion of specific viral and cellular components into exosomes, small endocytically derived vesicles that are released from cells. Exosomes produced by EBV-infected nasopharyngeal carcinoma cells contain high levels of the viral oncogene latent membrane protein 1 and viral microRNAs that activate critical signaling pathways in recipient cells. In this study, to determine the effects of EBV and KSHV on exosome content, quantitative proteomics techniques were performed on exosomes purified from 11 B-cell lines that are uninfected, infected with EBV or with KSHV, or infected with both viruses. Using mass spectrometry, 871 proteins were identified, of which ∼360 were unique to the viral exosomes. Analysis by 2D difference gel electrophoresis and spectral counting identified multiple significant changes compared with the uninfected control cells and between viral groups. These data predict that both EBV and KSHV exosomes likely modulate cell death and survival, ribosome function, protein synthesis, and mammalian target of rapamycin signaling. Distinct viral-specific effects on exosomes suggest that KSHV exosomes would affect cellular metabolism, whereas EBV exosomes would activate cellular signaling mediated through integrins, actin, IFN, and NFκB. The changes in exosome content identified in this study suggest ways that these oncogenic viruses modulate the tumor microenvironment and may provide diagnostic markers specific for EBV and KSHV associated malignancies.
Suppression of neointimal hyperplasia by sirolimus-eluting expanded polytetrafluoroethylene (ePTFE) haemodialysis grafts in comparison with paclitaxel-coated grafts.

BACKGROUND Haemodialysis vascular access dysfunction caused by aggressive venous neointimal hyperplasia is a major problem for haemodialysis patients with synthetic arteriovenous (AV) grafts. Several different strategies to prevent venous stenosis by inhibiting smooth muscle cell proliferation and migration using local delivery of potent antiproliferative agents are currently under investigation. We performed this study to evaluate the efficacy of sirolimus-eluting vascular grafts in preventing stenosis and to compare the effectiveness of sirolimus-coated grafts with that of paclitaxel-coated vascular grafts that we characterized in a previous study. METHODS AV grafts were implanted laterally between the common carotid artery and external jugular vein of 14 female Landrace pigs. Three types of grafts were implanted: grafts coated with 1.08 μg/mm(2) sirolimus (low dose, n = 6), grafts coated with 2.41 μg/mm(2) sirolimus (high dose, n = 2) and uncoated control grafts (n = 6). Animals were sacrificed 6 weeks after surgery. Cross-sections of the venous anastomoses were analysed to determine the percentage of luminal stenosis in each group, and immunohistochemistry was performed to identify the cellular phenotypes of the neointimal hyperplasia and tissues adjacent to the implanted grafts. RESULTS Compared with the control group, neointimal hyperplasia in the venous anastomoses of the groups implanted with sirolimus-coated vascular grafts was significantly suppressed without infection. The mean ± standard error values for the percentage of luminal stenosis were 75.7 ± 12.7% in the control group and 22.2 ± 1.41% in the low-dose sirolimus-coated group. Myofibroblasts and fibroblasts were the major cell types found in the neointimal hyperplasia. CONCLUSIONS Neointimal hyperplasia was effectively suppressed by sirolimus-eluting grafts. However, the inhibitory effects of sirolimus-eluting grafts were weaker than those observed for paclitaxel-coated grafts in our previous study.
FK506 inhibits the enhancing effects of transforming growth factor (TGF)‐β1 on collagen expression and TGF‐β/Smad signalling in keloid fibroblasts: implication for new therapeutic approach

Background Keloid is a unique proliferative disorder of fibroblasts resulting from derailment of the typical wound healing process. Due to lack of animal models for therapeutic testing, treatment of keloids remains a clinical challenge. Transforming growth factor (TGF)‐β1‐related signalling plays a key role in keloid formation. As tacrolimus (FK506) has been reported to inhibit the effects of TGF‐β1 on cultured fibroblasts, we hypothesized that FK506 may be useful in treating keloids.
Single-crystal structure determination of (Mg,Fe)SiO3 postperovskite

Knowledge of the structural properties of mantle phases is critical for understanding the enigmatic seismic features observed in the Earth’s lower mantle down to the core–mantle boundary. However, our knowledge of lower mantle phase equilibria at high pressure (P) and temperature (T) conditions has been based on limited information provided by powder X-ray diffraction technique and theoretical calculations. Here, we report the in situ single-crystal structure determination of (Mg,Fe)SiO3 postperovskite (ppv) at high P and after temperature quenching in a diamond anvil cell. Using a newly developed multigrain single-crystal X-ray diffraction analysis technique in a diamond anvil cell, crystallographic orientations of over 100 crystallites were simultaneously determined at high P in a coarse-grained polycrystalline sample containing submicron ppv grains. Conventional single-crystal structural analysis and refinement methods were applied for a few selected ppv crystallites, which demonstrate the feasibility of the in situ study of crystal structures of submicron crystallites in a multiphase polycrystalline sample contained within a high P device. The similarity of structural models for single-crystal Fe-bearing ppv (∼10 mol% Fe) and Fe-free ppv from previous theoretical calculations suggests that the Fe content in the mantle has a negligible effect on the crystal structure of the ppv phase.
Transcription of nephrin-Neph3 gene pair is synergistically activated by WT1 and NF-κB and silenced by DNA methylation.

BACKGROUND Nephrin and Neph3 are homologous molecules expressed in the podocyte slit diaphragms that are essential for normal glomerular ultrafiltration. Nephrin and Neph3 genes form a bidirectional gene pair suggesting that they may share key features in their regulation. We investigated if nephrin and Neph3 genes have similar mechanisms in their transcriptional regulation focussing on transcription factor Wilms' tumour 1 (WT1) and nuclear factor-κB (NF-κB) and DNA methylation. METHODS Transcriptional regulation of nephrin and Neph3 by WT1 and NF-κB was analysed by overexpression studies, reporter gene assay and chromatin immunoprecipitation using A293 cells and cultured podocytes. The interaction between WT1 and NF-κB was studied by co-immunoprecipitation. The effect of NF-κB activator tumour necrosis factor-α (TNF-α) with or without NF-κB pathway inhibitor (BAY 11-7082) on nephrin and Neph3 messenger RNA (mRNA) expression and on cellular distribution of NF-κB was determined by quantitative polymerase chain reaction (PCR) and immunostaining, respectively. The role of DNA methylation in regulating nephrin and Neph3 genes was studied by demethylating agent (5-aza-2'-deoxycytidine) treatment and quantitative PCR. RESULTS WT1 and NF-κB interact with nephrin and Neph3 promoter and cooperatively regulate nephrin and Neph3. The cooperation was further supported by the physical interaction between WT1 and NF-κB. TNF-α increased nephrin and Neph3 mRNA expression and this effect was mediated by NF-κB. Furthermore, DNA methylation played a role in silencing nephrin and Neph3 expression in a cell-type and differentiation stage-dependent manner. CONCLUSION These results provide novel insights into the transcriptional regulation of nephrin and Neph3 genes and indicate that nephrin and Neph3 share the same mechanisms in their regulation.
Solution coating around ice particles of incipient cirrus clouds

Kuhs et al. (1) report on the nanometer-scale roughness on the surface of laboratory vapor-deposited cubic ice, Ic, and state that such roughness on the surface of cirrus Ic ice particles can influence the surface reactivity, radiative properties, and water vapor uptake coefficient of incipient cirrus clouds. This assumes that the ice surface of cirrus particles is exposed to air. However, this is not the case when cirrus particles are formed by freezing aqueous aerosol drops. Freezing of aqueous drops with ∼20–40 wt% of solute is the mechanism discussed in literature studies mentioned by Kuhs et al., i.e., their refs. 20, 55, 58, and 59.
Progressive hearing loss and gradual deterioration of sensory hair bundles in the ears of mice lacking the actin-binding protein Eps8L2

Mechanotransduction in the mammalian auditory system depends on mechanosensitive channels in the hair bundles that project from the apical surface of the sensory hair cells. Individual stereocilia within each bundle contain a core of tightly packed actin filaments, whose length is dynamically regulated during development and in the adult. We show that the actin-binding protein epidermal growth factor receptor pathway substrate 8 (Eps8)L2, a member of the Eps8-like protein family, is a newly identified hair bundle protein that is localized at the tips of stereocilia of both cochlear and vestibular hair cells. It has a spatiotemporal expression pattern that complements that of Eps8. In the cochlea, whereas Eps8 is essential for the initial elongation of stereocilia, Eps8L2 is required for their maintenance in adult hair cells. In the absence of both proteins, the ordered staircase structure of the hair bundle in the cochlea decays. In contrast to the early profound hearing loss associated with an absence of Eps8, Eps8L2 null-mutant mice exhibit a late-onset, progressive hearing loss that is directly linked to a gradual deterioration in hair bundle morphology. We conclude that Eps8L2 is required for the long-term maintenance of the staircase structure and mechanosensory function of auditory hair bundles. It complements the developmental role of Eps8 and is a candidate gene for progressive age-related hearing loss.
Polymer/Perovskite Amplifying Waveguides for Active Hybrid Silicon Photonics

The emission properties of hybrid halide perovskites are exploited to implement a stable and very low power operation waveguide optical amplifier integrated in a silicon platform. By optimizing its design with a poly(methyl methacrylate) (PMMA) encapsulation, this novel photonic device presents a net gain of around 10 dB cm(-1) and 3-4 nm linewidth with an energy threshold as low as 2 nJ pulse(-1) and exhibiting no degradation after one year.
Highly Elastic and Conductive Human‐Based Protein Hybrid Hydrogels

A highly elastic hybrid hydrogel of methacryloyl-substituted recombinant human tropoelastin (MeTro) and graphene oxide (GO) nanoparticles are developed. The synergistic effect of these two materials significantly enhances both ultimate strain (250%), reversible rotation (9700°), and the fracture energy (38.8 ± 0.8 J m(-2) ) in the hybrid network. Furthermore, improved electrical signal propagation and subsequent contraction of the muscles connected by hybrid hydrogels are observed in ex vivo tests.
Mammalian cells preferentially internalize hydrogel nanodiscs over nanorods and use shape-specific uptake mechanisms

Significance Nanoparticles are widely investigated for intracellular drug delivery and molecular imaging and should be designed to maximize cell uptake. Here the effects of particle geometry to maximize nanoparticle uptake by mammalian cells are evaluated. The findings show that uptake is governed by a combination of cell–particle adhesion, strain energy for membrane wrapping around the particle, and local particle concentration at the cell membrane, all of which are particle-shape–dependent. Under typical culture conditions, disc-shaped hydrophilic nanoparticles were internalized more efficiently than nanorods. Interestingly, larger nanodiscs and rods had higher uptake compared with the smallest particles tested. Mechanisms of uptake were also shape- and cell type-specific. These results provide important insights for rational design of nanocarriers to maximize intracellular delivery efficacy. Size, surface charge, and material compositions are known to influence cell uptake of nanoparticles. However, the effect of particle geometry, i.e., the interplay between nanoscale shape and size, is less understood. Here we show that when shape is decoupled from volume, charge, and material composition, under typical in vitro conditions, mammalian epithelial and immune cells preferentially internalize disc-shaped, negatively charged hydrophilic nanoparticles of high aspect ratios compared with nanorods and lower aspect-ratio nanodiscs. Endothelial cells also prefer nanodiscs, however those of intermediate aspect ratio. Interestingly, unlike nanospheres, larger-sized hydrogel nanodiscs and nanorods are internalized more efficiently than their smallest counterparts. Kinetics, efficiency, and mechanisms of uptake are all shape-dependent and cell type-specific. Although macropinocytosis is used by both epithelial and endothelial cells, epithelial cells uniquely internalize these nanoparticles using the caveolae-mediated pathway. Human umbilical vein endothelial cells, on the other hand, use clathrin-mediated uptake for all shapes and show significantly higher uptake efficiency compared with epithelial cells. Using results from both upright and inverted cultures, we propose that nanoparticle internalization is a complex manifestation of three shape- and size-dependent parameters: particle surface-to-cell membrane contact area, i.e., particle–cell adhesion, strain energy for membrane deformation, and sedimentation or local particle concentration at the cell membrane. These studies provide a fundamental understanding on how nanoparticle uptake in different mammalian cells is influenced by the nanoscale geometry and is critical for designing improved nanocarriers and predicting nanomaterial toxicity.
Trends in immune function assay (ImmuKnow; Cylex™) results in the first year post-transplant and relationship to BK virus infection.

BACKGROUND The ImmuKnow assay is a functional T-cell assay (TCA) that may quantify cellular immune responsiveness following renal transplantation. Using a standard protocol of TCA sampling in the first year post-transplant, we examined changes in TCA values over time and tested for an association between TCA and BK virus (BKV) infection as a marker of over-immunosuppression. METHODS We performed a single-center retrospective analysis of 897 TCA results in 414 renal transplant recipients obtained at 0 (N = 122), 1 (N = 316), 6 (N = 258) and 12 (N = 201) months post-transplant from May 2005 to July 2009 with concurrent urine and blood BKV polymerase chain reaction measurements. RESULTS Nearly 40% of patients experienced a decrease in TCA of >150 ng/mL from 1 to 6 months (mean 466-356 ng/mL, P < 0.0001) and remained stable from 6 to 12 months (mean 357 versus 370 ng/mL, P = 0.33). Neither a change in TCA of >150 ng/mL nor a TCA value of ≤ 225 ng/mL were associated with a diagnosis of BKV infection at 1 or 6 months, while TCA ≤ 225 ng/mL was associated with BKV infection at 12 months (P = 0.005). CONCLUSIONS A reduction in TCA from 1 to 6 months post-transplant is common and is not associated with conditions of over-immunosuppression, rendering the interpretation of changes in TCA during this time period difficult. BKV infection is associated with low TCA values at 12 months, suggesting that patients with low TCA values after 6 months may benefit from potential tailoring of immunosuppression or more aggressive monitoring to prevent subsequent BKV infection.
Microfluidic Bioprinting of Heterogeneous 3D Tissue Constructs Using Low‐Viscosity Bioink

A novel bioink and a dispensing technique for 3D tissue-engineering applications are presented. The technique incorporates a coaxial extrusion needle using a low-viscosity cell-laden bioink to produce highly defined 3D biostructures. The extrusion system is then coupled to a microfluidic device to control the bioink arrangement deposition, demonstrating the versatility of the bioprinting technique. This low-viscosity cell-responsive bioink promotes cell migration and alignment within each fiber organizing the encapsulated cells.
Educational and motivational support service: a pilot study for mobile‐phone‐based interventions in patients with psoriasis

Background Psoriasis is a chronic disease which requires long‐term therapy. Therefore, adherence to therapy and patient motivation are key points in controlling the disease. Mobile‐phone‐based interventions, and in particular text messages (TM), have already been used effectively to motivate patients and improve treatment adherence in many different chronic diseases such as diabetes, cardiovascular disease and asthma.
The risk of cancer in people with diabetes and chronic kidney disease.

BACKGROUND Diabetes and chronic kidney disease (CKD) are both associated with an increased risk of cancer but it is unclear whether diabetes complicated by CKD further augments an individual's cancer risk. The aim of our study was to determine the association of CKD [defined as an estimated glomerular filtration rate (eGFR) < 60 mL/min] with the overall and site-specific risks of incident cancers among individuals with Type 2 diabetes. METHODS Cox proportional hazard regression models and competing risk analyses were used to examine the univariate and multivariate adjusted associations between reduced kidney function and the overall and site-specific risks of cancer in participants enrolled in the Action in Diabetes and Vascular disease: Preterax and Diamicron MR controlled evaluation (ADVANCE) trial. RESULTS Over a median follow-up of 5.0 years, 700 malignant neoplasms occurred in the 11 140 (6.4%) participants. There was no increase in overall cancer risk [adjusted hazard ratio: 1.07 (95% confidence interval: 0.89-1.29, P = 0.50)] or site-specific cancer risk for individuals with CKD (defined as eGFR < 60 mL/min) compared to those without CKD at baseline. These results were robust to multiple methods and thresholds used to estimate CKD. CONCLUSIONS Mild to moderate CKD does not increase the risk of cancer in people with Type 2 diabetes. ADVANCE is registered with ClincalTrial.gov (number NCT00145925).