Methylation-assisted bisulfite sequencing to simultaneously map 5fC and 5caC on a genome-wide scale for DNA demethylation analysis.

Active DNA demethylation is mediated by ten-eleven translocation (TET) proteins that progressively oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). We have developed a methylation-assisted bisulfite sequencing (MAB-seq) method that enables direct genome-scale mapping and quantification of 5fC and 5caC marks together at single-base resolution. In bisulfite sequencing (BS), unmethylated cytosine residues (Cs), 5fCs and 5caCs, are converted to uracil and cannot be discriminated from each other.

Adding Liver Stiffness Measurement to the Routine Evaluation of Hepatocellular Carcinoma Resectability Can Optimize Clinical Outcome.

 Liver stiffness (LS) has been shown to be of use in chronic liver disease patients but its utility in surgical judgment still needs to be proven. A decision-making approach was applied to evaluate whether LS measurement before surgery of hepatocellular carcinoma (HCC) can be useful in avoiding post-hepatectomy liver failure (PHLF).  Decision curve analysis (DCA) was applied to 202 HCC patients (2008 - 14) with LS measurement prior to hepatectomy to verify whether the occurrence of PHLF grades B/C should be reduced through a decision-making approach with LS.

Coronary Microvascular Dysfunction Predicts Long-Term Outcome in Simultaneous Pancreas-Kidney Transplantation.

Background: Patients with diabetes are at increased cardiovascular risk. Simultaneous pancreas-kidney transplantation (SPKT) is the treatment of choice in patients with type 1 diabetes mellitus and diabetic nephropathy. We assessed coronary flow reserve (CFR) by transthoracic echocardiography as a marker of major adverse cardiac events (MACE) in SPKT patients.

Body experiences and psychopathology in idiopathic central precocious and early puberty.

Background: Idiopathic central precocious (PP) and early puberty (EP) are frequently associated with psychopathological problems. The aim of this study was to evaluate the quality of body experiences and psychological aspects in girls with PP and EP, as well as the impact of these conditions on their families and the subjects' vulnerability.

Methods: Subjects with PP or EP, aged 7-15 years, were evaluated through the administration of a self-report questionnaire (Children's Depression Inventory, CDI), along with a projective test (Human Figure Drawing Test, HFDT).

A micro-Raman spectroscopic investigation of leukemic U-937 cells in aged cultures.

Recently it has been shown that micro-Raman spectroscopy combined with multivariate analysis is able to discriminate among different types of tissues and tumoral cells by the detection of significant alterations and/or reorganizations of complex biological molecules, such as nucleic acids, lipids and proteins. Moreover, its use, being in principle a non-invasive technique, appears an interesting clinical tool for the evaluation of the therapeutical effects and of the disease progression. In this work we analyzed molecular changes in aged cultures of leukemia model U937 cells with respect to fresh cultures of the same cell line.

Laser light triggered smart release of silibinin from a PEGylated-PLGA gold nanocomposite.

In this work a new remotely-triggered drug delivery system based on PEG-PLGA_Au nanocomposite is proposed. Due to the optical properties of gold nanoparticles (Au NPs), the nanovector allows on-demand control of the dose, the timing and the duration of the drug release, upon irradiation with red laser light. The Au NPs are synthesized by laser ablation and subsequently embedded into the PEG-PLGA copolymer via a modified emulsion-diffusion method, devised in such a way that both Au NPs and silibinin (SLB), a flavonolignan with promising anti-neoplastic effects, can be co-loaded into the polymeric system in a single step procedure.

RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data.

Summary: The rapidly increasing number of discovered non-coding RNAs makes the understanding of their structure a key feature toward a deeper comprehension of gene expression regulation. Various enzymatic- and chemically- based approaches have been recently developed to allow whole-genome studies of RNA secondary structures. Several methods have been recently presented that allow high-throughput RNA structure probing (CIRS-seq, Structure-seq, SHAPE-seq, PARS, etc.

Snai1 represses Nanog to promote embryonic stem cell differentiation.

Embryonic stem cell (ESC) self-renewal and pluripotency is maintained by an external signaling pathways and intrinsic regulatory networks involving ESC-specific transcriptional complexes (mainly formed by OCT3/4, Sox2 and Nanog proteins), the Polycomb repressive complex 2 (PRC2) and DNA methylation [1-8]. Among these, Nanog represents the more ESC specific factor and its repression correlates with the loss of pluripotency and ESC differentiation [9-11]. During ESC early differentiation, many development-associated genes become upregulated and although, in general, much is known about the pluripotency self-renewal circuitry, the molecular events that lead ESCs to exit from pluripotency and begin differentiation are largely unknown.

High-throughput whole-genome sequencing of E14 mouse embryonic stem cells.

Mouse E14 embryonic stem cells (ESCs) are the most used ESC line, often employed for genome-wide studies involving next generation sequencing analysis [1-5]. More than 2 × 10 E9 sequences made on Illumina platform derived from the genome of E14 embryonic stem cells cultured in our laboratory were used to build a database of about 2.7 × 10 E6 single nucleotide variant [6].

Liver metastases from non-gastrointestinal non-neuroendocrine tumours: review of the literature.

Liver resection is integrated in the oncological surgical management of metastatic gastrointestinal and neuroendocrine tumours. However, the good prognosis reached in these cases has not been obtained for metastatic tumours of other histological types. In this review, we analysed the published case reports and series of hepatectomies in patients with metastatic breast cancer, melanoma, sarcoma, genitourinary tumours, pulmonary and adrenocortical tumours.

Hepatic venous pressure gradient in the preoperative assessment of patients with resectable hepatocellular carcinoma.

Backgrounds & Aims: To assess the relationship existing between hepatic venous pressure gradient (HVPG) and the occurrence of post-hepatectomy liver failure (PHLF) grade B/C after resection of hepatocellular carcinoma (HCC) and persistent worsening of liver function.

Methods: Data from 70 consecutive prospectively enrolled HCC patients undergoing resection were collected and analysed. PHLF grade B/C was defined by the International Study Group of Liver Surgery recommendations.

Improving memory following prefrontal cortex damage with the PQRST method.

We tested (1) whether the PQRST method, involving Preview (P), Question (Q), Read (R), State (S), and Test (T) phases, is effective in enhancing long-term memory in patients with mild memory problems due to prefrontal cortex lesions, and (2) whether patients also benefit from a more self-initiated version of the PQRST. Seven patients with prefrontal lesions encoded new texts under three different conditions: the Standard condition, requiring to read texts repeatedly, the PQRST-Other condition, in which the experimenter formulated questions about the text (Q phase), and the PQRST-Self condition, in which patients formulated the relevant questions on their own. Compared to the Standard condition, both the PQRST-Other and the PQRST-Self condition resulted in higher immediate and delayed recall rates, as well as a higher ability to answer questions about the texts.

Stabilization of Titanium Dioxide Nanoparticles at the Surface of Carbon Nanomaterials Promoted by Microwave Heating.

TiO2 is frequently combined with carbon materials, such as reduced graphene oxide (RGO), to produce composites with improved properties, for example for photocatalytic applications. It is shown that heating conditions significantly affect the interface and photocatalytic properties of TiO2 @C, and that microwave irradiation can be advantageous for the synthesis of carbon-based materials. Composites of TiO2 with RGO or amorphous carbon were prepared from reaction of titanium isopropoxide with benzyl alcohol.

Chemical Modification of Graphene Oxide through Diazonium Chemistry and Its Influence on the Structure-Property Relationships of Graphene Oxide-Iron Oxide Nanocomposites.

4-Carboxyphenyl groups are covalently grafted onto graphene oxide via diazonium chemistry for studying their role on the adsorption of iron oxide nanoparticles. The nanoparticles are deposited via a novel phase-transfer approach involving specific interactions at the interface between two immiscible solvents. The increased density and the homogeneous distribution of surface carboxyl moieties enable the preparation of a nanocomposite with improved iron oxide distribution and loading.

Gain of hTERC: a genetic marker of malignancy in oral potentially malignant lesions.

Oral squamous cell carcinoma (OSCC) is the most common oral cancer, and major efforts is being made to identify molecular markers capable to differentiate oral potentially malignant lesions (OPMLs) with indolent course from lesions with aggressive behavior. We undertook a study to evaluate if gain of the human telomerase RNA component (hTERC) gene in OPMLs could indicate lesions at high risk of developing OSCC. The study was performed on 30 OPMLs with long-term follow-up using a dual-color interphase fluorescence in situ hybridization (FISH) for hTERC status.

Phage-AgNPs complex as SERS probe for U937 cell identification.

The early diagnosis of malignancy is the most critical factor for patient survival and the treatment of cancer. In particular, leukemic cells are highly heterogeneous, and there is a need to develop new rapid and accurate detection systems for early diagnosis and monitoring of minimal residual disease. This study reports the utilization of molecular networks consisting of entire bacteriophage structure, displaying specific peptides, directly assembled with silver nanoparticles as a new Surface Enhanced Raman Spectroscopy (SERS) probe for U937 cells identification in vitro.

Subject-Based versus Population-Based Care after Radiation Exposure.

In a mass casualty radiation event situation, individualized therapy may overwhelm available resources and feasibility issues suggest a need for the development of population-based strategies. To investigate the efficacy of a population-based strategy, Chinese macaques (n = 46) underwent total-body irradiation and received preemptive antibiotics, IV hydration on predetermined postirradiation days and were then compared to macaques (n = 48) that received subject-based care in which blood transfusions, IV hydration, nutritional supplementation and antibiotic supportive measures were provided. Estimated radiation doses for LD30/60, LD50/60 and LD70/60 of animals with subject-based care: 6.

Beta-amyloid plasma levels in adolescents with anorexia nervosa of the restrictive type.

Background: Reduced plasma leptin and elevated homocysteine (Hcy) are known to lead to increased β-amyloid (Aβ) production, besides being hallmarks of anorexia nervosa (AN) of the restrictive type. AN subjects display several neuropsychiatric manifestations, which may entail Aβ-mediated altered synaptic functions. The aim of this study consisted in assessing Aβ plasma levels in AN patients.

TET1 is controlled by pluripotency-associated factors in ESCs and downmodulated by PRC2 in differentiated cells and tissues.

Ten-eleven translocation (Tet) genes encode for a family of hydroxymethylase enzymes involved in regulating DNA methylation dynamics. Tet1 is highly expressed in mouse embryonic stem cells (ESCs) where it plays a critical role the pluripotency maintenance. Tet1 is also involved in cell reprogramming events and in cancer progression.

AKI Recovery Induced by Mesenchymal Stromal Cell-Derived Extracellular Vesicles Carrying MicroRNAs.

Phenotypic changes induced by extracellular vesicles have been implicated in mesenchymal stromal cell-promoted recovery of AKI. MicroRNAs are potential candidates for cell reprogramming toward a proregenerative phenotype. The aim of this study was to evaluate whether microRNA deregulation inhibits the regenerative potential of mesenchymal stromal cells and derived extracellular vesicles in a model of glycerol-induced AKI in severe combined immunodeficient mice.

Global and regional brain volumes normalization in weight-recovered adolescents with anorexia nervosa: preliminary findings of a longitudinal voxel-based morphometry study.

The recent literature on anorexia nervosa (AN) suggests that functional and structural abnormalities of cortico-limbic areas might play a role in the evolution of the disease. We explored global and regional brain volumes in a cross-sectional and follow-up study on adolescents affected by AN. Eleven adolescents with AN underwent a voxel-based morphometry study at time of diagnosis and immediately after weight recovery.

Immunosuppression Modifications Based on an Immune Response Assay: Results of a Randomized, Controlled Trial.

Background: An immune function assay shows promise for identifying solid organ recipients at risk for infection or rejection. The following randomized prospective study was designed to assess the clinical benefits of adjusting immunosuppressive therapy in liver recipients based on immune function assay results.

Methods: Adult liver recipients were randomized to standard practice (control group; n = 102) or serial immune function testing (interventional group; n = 100) performed with a commercially available in vitro diagnostic assay (ImmuKnow; Viracor-IBT Laboratories, Lee's Summit, MO) before transplantation, immediately after surgery and at day 1, weeks 1 to 4, 6, and 8, and months 3 to 6, 9, and 12.

Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics.

Ten eleven translocation (Tet) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be further excised by thymine-DNA glycosylase (Tdg). Here, we present a genome-wide approach, named methylation-assisted bisulfite sequencing (MAB-seq), that enables single-base resolution mapping of 5fC and 5caC and measures their abundance.

Snai1 promotes ESC exit from the pluripotency by direct repression of self-renewal genes.

Although much is known about the pluripotency self-renewal circuitry, the molecular events that lead embryonic stem cells (ESCs) exit from pluripotency and begin differentiation are largely unknown. We found that the zinc finger transcription factor Snai1, involved in gastrulation and epithelial-mesenchymal transition, is already expressed in the inner cell mass of the preimplantation blastocysts. In ESCs, Snai1 does not respond to TGFβ or BMP4 signaling but it is induced by retinoic acid treatment, which induces the binding, on the Snai1 promoter, of the retinoid receptors RARγ and RXRα, the dissociation of the Polycomb repressor complex 2 which results in the decrease of H3K27me3, and the increase of histone H3K4me3.