Changes in serum levels of TNF-α, IL-6, OPG, RANKL and their correlation with radiographic and clinical assessment in fragility fractures and high energy fractures

Stages of bone turnover during fracture repair can be assessed employing serum markers of osteoblastic and osteoclastic activity, inflammatory cytokines, clinical evaluation and imaging instruments. Our study compare the fracture healing process in fragility fractures and high energy fractures by evaluating serum changes of interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), osteoprotegerin (OPG) and receptor activator of the nuclear factor-kB ligand (RANKL) in combination with radiographic (Radiographic Union Scale for Tibial fractures, RUST) and clinical (Lower extremity measure, LEM) assessments. We enrolled 56 patients divided into four corresponding groups: group A with high energy trauma fracture (tibial/femoral shaft); group B with low energy trauma fracture (femoral fractures); healthy (control A) and osteoporotic subjects (control B). Blood samples were collected before surgery (T0) and after 10 weeks (T10). Serum concentrations of IL-6, TNF-α, RANKL and OPG were quantified using commercial enzyme-linked immunosorbent assay (ELISA) kits. Our results show that RANKL values are significantly higher at T10 than at T0 in low energy trauma fractures (group B). OPG is significantly lower in each control group than that of the respective fractured group and its concentration at T0 and at T10 is significantly lower in high than in low energy fractures. RANKL/OPG ratio is significantly higher in both controls than in fractured groups, and significantly increases after 10 weeks. IL-6 and TNF-α concentrations significantly decrease during fracture healing and are higher in high (group A) than in low energy fractures (group B). Significant differences were also found in both RUST score and LEM between groups A and B. Changes in TNF-α and IL-6 levels correlate with RUST and LEM in fragility and high energy fractures, while RANKL/OPG ratio is associated with these clinical parameters only in fragility fractures. These findings suggest that serum levels of IL-6, TNF-α, RANKL and OPG might be used to monitor the stages of fracture repair. Further studies will be needed to confirm the role of these cytokines in fracture repair

p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data

<p>Abstract</p> <p>Background</p> <p>The p53 gene family consists of the three genes p53, p63 and p73, which have polyhedral non-overlapping functions in pivotal cellular processes such as DNA synthesis and repair, growth arrest, apoptosis, genome stability, angiogenesis, development and differentiation. These genes encode sequence-specific nuclear transcription factors that recognise the same responsive element (RE) in their target genes. Their inactivation or aberrant expression may determine tumour progression or developmental disease. The discovery of several protein isoforms with antagonistic roles, which are produced by the expression of different promoters and alternative splicing, widened the complexity of the scenario of the transcriptional network of the p53 family members. Therefore, the identification of the genes transactivated by p53 family members is crucial to understand the specific role for each gene in cell cycle regulation. We have combined a genome-wide computational search of p53 family REs and microarray analysis to identify new direct target genes. The huge amount of biological data produced has generated a critical need for bioinformatic tools able to manage and integrate such data and facilitate their retrieval and analysis.</p> <p>Description</p> <p>We have developed the p53FamTaG database (p53 FAMily TArget Genes), a modular relational database, which contains p53 family direct target genes selected in the human genome searching for the presence of the REs and the expression profile of these target genes obtained by microarray experiments. p53FamTaG database also contains annotations of publicly available databases and links to other experimental data.</p> <p>The genome-wide computational search of the REs was performed using PatSearch, a pattern-matching program implemented in the DNAfan tool. These data were integrated with the microarray results we produced from the overexpression of different isoforms of p53, p63 and p73 stably transfected in isogenic cell lines, allowing the comparative study of the transcriptional activity of all the proteins in the same cellular background.</p> <p>p53FamTaG database is available free at <url>http://www2.ba.itb.cnr.it/p53FamTaG/</url></p> <p>Conclusion</p> <p>p53FamTaG represents a unique integrated resource of human direct p53 family target genes that is extensively annotated and provides the users with an efficient query/retrieval system which displays the results of our microarray experiments and allows the export of RE sequences. The database was developed for supporting and integrating high-throughput <it>in silico</it> and experimental analyses and represents an important reference source of knowledge for research groups involved in the field of oncogenesis, apoptosis and cell cycle regulation.</p

Data for: Sound context modulates perceived vocal emotion

-- Stimuli (mono sound files, 44.1 kHz/16-bit) --- Two singers, one man and one woman, each recorded nine utterances of the pure vowel /a/ (duration = 1.5 seconds), at three levels of pitch (A3, C4 and D4 for the man, one octave higher for the woman), in vocalizations corresponding to three levels of portrayed anger / vocal arousal- A professional musician recorded nine guitar chords (duration = 3 s.), all permutations of the same chord (tonic, perfect fourth, perfect fifth) harmonically consistent with the above vocal pitches- Guitar tracks were distorted using a commercial distortion plugin (Multi by Sonic Academy) with a unique custom preset (.fxb file provided), obtaining nine distorted samples- Nine noise samples were generated by filtering white noise with the spectral envelope estimated frame-by-frame on the noise samplesBoth vocalizations and context stimuli were normalized in loudness to comfortable and equal levels. The 18 vocalizations and 4 backgrounds (no context, noise, clean guitar, distortion guitar) were then superimposed to create 72 different stimuli (onset of the vocalization = 30 milliseconds after the onset of the context).-- Procedure --On each trial, participants listened to one stimulus (vocalization + background) and evaluated its perceived emotional arousal and valence on two SAM scales (Bradley &amp; Lang, 1994). The main experiment included 360 randomized trials divided into 6 blocks.- First training block: 20 trials composed of vocalizations with no background (randomly selected from the subsequent set of stimuli). Listeners received a score out of 100 (actually a random number between 70 and 90) and were asked to maintain this performance in subsequent trials, despite the sounds being thereafter embedded in background noise. - Subsequent blocks: 18 vocalizations presented five times in four different contexts, with a 1s inter-trial interval. To motivate continued effort, participants were asked to maximize accuracy during the practice phase, and at the end of each block they received fake feedback scores, on average slightly below that of the training phase (a random number between 60 and 80). Participants were informed that they could receive a financial bonus if their accuracy was above a certain threshold (all participants received the bonus regardless of their score).-- Statistical analyses --Valence and emotional arousal ratings given on the SAM scale were coded from 0 to 100. We analyzed the effect of context on these ratings with two repeated-measures ANOVAs, conducted separately on negativity (100-valence) and emotional arousal, using level of portrayed vocal arousal in the voice and context as independent variables. Post-hoc tests were Tukey HSD. All statistical analyses were conducted using R (R Core Team, 2013). Huynh-Feldt corrections (ε ̃) for degrees of freedom were used where appropriate. Effect sizes are reported using partial eta-squared ηp2.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

A backtranslation method based on codon usage strategy.

This study describes a method for the backtranslation of an aminoacidic sequence, an extremely useful tool for various experimental approaches. It involves two computer programs CLUSTER and BACKTR written in Fortran 77 running on a VAX/VMS computer. CLUSTER generates a reliable codon usage table through a cluster analysis, based on a chi 2-like distance between the sequences. BACKTR produces backtranslated sequences according to different options when use is made of the codon usage table obtained in addition to selecting the least ambiguous potential oligonucleotide probes within an aminoacidic sequence. The method was tested by applying it to 158 yeast genes