Miracle-dz/UniFAR-FTUs huggingface dataset:
Hormones as Stimuli for Muscle Growth

Skeletal muscle is affected by many hormones and growth factors, both catabolic and anabolic in nature. Our understanding of the synthesis, release, transport and tissue sensitivities of these hormones has increased greatly in recent years. Despite this knowledge we still do not know the link between hormonal/growth factor release, training and muscle hypertrophy. The hormonal response to high resistance exercise involves an acute increase in cortisol, GH, testosterone, and catecholamines and a decrease or no change in insulin and thyroid status. In the longer term there may also be changes in muscle sensitivity. Much attention has focused on the anabolic effects of androgens. The evidence that exogenous derivatives of testosterone are anabolic in eugonadal men is still controversial. In supraphysiological doses, and combined with training, there is some evidence for their anabolic effects. This needs to be weighed against their potentially harmful side-effects. Studies on GH replacement in GH-deficiency strongly indicated an important role for GH in the maintenance of lean tissue mass. Despite its role in clinical situations, the controlled trials have failed to demonstrate a clear anabolic role for GH in either the healthy younger or older person. A likely candidate for causing muscle hypertrophy as a result of resistance training, is IGF1. This would appear to be independent of GH release and act in an autoocrine/paracrine fashion. A splice variant if IGF-1 has been identified and is expressed locally in muscle during repair and overload. This mechano growth factor (MGF) may be an important factor linking a mechanical stimulus and growth. More recently there has been renewed interest in searching for an “anabolic hormone” due to the increasing numbers of elderly people within populations and the associated frailty common in this group. Reduced physical activity levels and a shifting anabolic/catabolic ratio all contribute to this problem.
A controlled study on the effectiveness of EEG biofeedback on attention deficit hyperactivity disorder

Objective To explore the effectiveness and the characteristics of EEG biofeedback treatment on attention deficit hyperactivity disorder (ADHD) Methods Fifty seven children with ADHD diagnosed according to the DSM Ⅲ R criteria were enrolled in the study They were randomly assigned to the EEG biofeedback treatment (EEG) group (28 cases) and the Ritalin (MED) treatment group (29 cases) They were evaluated before, during, and after treatment with Conner′s behavior rating scale, side effects scale, Wechsler Intelligence Scale, TOVA, and Quantitative EEG All the subjects were followed up in one to three months after treatment Results (1) The score of Conner′s Rating Scale decreased significantly in both groups The MED group showed a relatively more decrease of scores in the behavior scale, but rebounded when the treatment stopped (hyperactivity index score for example: pretreatment 16 14±4 64,post treatment 4 23±1 45,follow up 13 52±5 08), while the EEG group showed a continual improvement (hyperactivity index: pretreatment 16 04±6 31, post treatment 9 26± 3 09, follow up 8 76±3 79) Side effects emerged more frequently (82%) in MED group but none in EEG group (2) Both groups improved significantly on the Omission and Commission level of TOVA ( P 0 05), the MED group made a significant improvement on Variability of Response to medicine ( P 0 01) In follow up, the advantage was replaced and became even worse on Omission compared to pretreatment The EEG group improved continuously (3) The EEG group gained a significant increase in score of the Free from Distractibility Factor of Wechsler Intelligence Scale (pretreatment 93 7±13 3,follow up 106 3±14 1, P 0 01) (4) A significant increase of relative power of 8 13 Hz waves and decrease of 0 4 Hz waves was found in EEG group through the Quantitative EEG No such results were found in MED group Conclusion The effectiveness of EEG biofeedback is affirmed Compared to the psycho stimulant Ritalin, it shows slower but relatively permanent effects, and a special effect on improving of attention and the EEG spectrum
Learning to identify CNS drug action and efficacy using multistudy fMRI data

Existing functional brain imaging data sets were used to identify neural signatures that confirm pharmacological action and predict clinical efficacy of test compounds. Brain patterns determine drug efficacy There are many drugs out there that affect the central nervous system (CNS), from drugs for chronic pain to schizophrenia to obesity. A brain imaging technique called functional magnetic resonance imaging (fMRI) has shown promise for distinguishing an effective compound from an ineffective one, but the real unmet need is to be able to predict whether a new CNS drug will have clinical efficacy. To this end, Duff et al. evaluated existing fMRI data sets for patients who were exposed to painful stimuli (such as heat or a squeeze) and given either an analgesic compound or a placebo. From these brain “maps,” or neural signatures, the authors were able to create a general “stop/go” decision-making framework—which included quality assurance, pharmacodynamic effect, and evidence for clinical efficacy steps—that allowed them to determine whether the signature of a new compound provided evidence for analgesic properties. Other than evaluating potential drug efficacy, the authors revealed insights into pain response mechanisms. This multistudy approach by Duff et al. may translate to a powerful tool in synthesizing and learning from neuroimaging data to improve—and perhaps speed up—CNS drug discovery and repurposing. The therapeutic effects of centrally acting pharmaceuticals can manifest gradually and unreliably in patients, making the drug discovery process slow and expensive. Biological markers providing early evidence for clinical efficacy could help prioritize development of the more promising drug candidates. A potential source of such markers is functional magnetic resonance imaging (fMRI), a noninvasive imaging technique that can complement molecular imaging. fMRI has been used to characterize how drugs cause changes in brain activity. However, variation in study protocols and analysis techniques has made it difficult to identify consistent associations between subtle modulations of brain activity and clinical efficacy. We present and validate a general protocol for functional imaging–based assessment of drug activity in the central nervous system. The protocol uses machine learning methods and data from multiple published studies to identify reliable associations between drug-related activity modulations and drug efficacy, which can then be used to assess new data. A proof-of-concept version of this approach was developed and is shown here for analgesics (pain medication), and validated with eight separate studies of analgesic compounds. Our results show that the systematic integration of multistudy data permits the generalized inferences required for drug discovery. Multistudy integrative strategies of this type could help optimize the drug discovery and validation pipeline.
Radiographic evaluation of the symphysis menti as a donor site for an autologous bone graft in pre-implant surgery

Purpose This study was performed to obtain a quantitative evaluation of the cortical and cancellous bone graft harvestable from the mental and canine regions, and to evaluate the cortical vestibular thickness. Materials and Methods This study collected cone-beam computed tomographic (CBCT) images of 100 Italian patients. The limits of the mental region were established: 5 mm in front of the medial margin of each mental foramen, 5 mm under the apex of each tooth present, and above the inferior mandibular cortex. Cortical and cancellous bone volumes were evaluated using SimPlant software (SimPlant 3-D Pro, Materialize, Leuven, Belgium) tools. In addition, the cortical vestibular thickness (minimal and maximal values) was evaluated in 3 cross-sections corresponding to the right canine tooth (3R), the median section (M), and the left canine tooth (3L). Results The cortical volume was 0.71±0.23 mL (0.27-1.96 mL) and the cancellous volume was 2.16±0.76 mL (0.86-6.28 mL). The minimal cortical vestibular thickness was 1.54±0.41 mm (0.61-3.25 mm), and the maximal cortical vestibular thickness was 3.14±0.75mm(1.01-5.83 mm). Conclusion The use of the imaging software allowed a patient-specific assessment of mental and canine region bone availability. The proposed evaluation method might help the surgeon in the selection of the donor site by the comparison between bone availability in the donor site and the reconstructive exigency of the recipient site.
The Sociological Vision of Pierre Bourdieu

Prefatory note The paper reprinted here grew out of a close reading of Bourdieu’s work undertaken while writing an M.A. thesis on Bourdieu at the University of Sussex in 1980. At that time, La Distinction (1979) and Le Sens pratique (1980) had just been published in French. The first statement of Bourdieu’s general theoretical stance had been translated in 1977 as Outline of a Theory of Practice, but the only other books available in English dealt with Algeria or with education. Several important articles and book chapters by Bourdieu had been published in English, but these were not widely known or readily accessible. Only a few articles about Bourdieu’s work had appeared in English. In the English-speaking world, anthropologists and sociologists of education were familiar with the work, but broader audiences in the social sciences and humanities were not. Five years later, when the paper was published in Theory and Society, this had already begun to change. Distinction appeared in English in 1984, and wider audiences were becoming interested in Bourdieu’s work. In subsequent years, of course, virtually all of Bourdieu’s major work has become available in English, and a large secondary literature has developed. And Bourdieu’s own oeuvre continued to grow in rich new directions, yielding such important books as Homo Academicus, The State Nobility, Pascalian Meditations ,a ndThe Rules of Art. This paper should be understood in context, then, as an early attempt in English to come to terms with Bourdieu’s work, and particularly with Distinction, through an analysis of the systematic metatheory that, I argued, informed all Bourdieu’s work up to that point. CHAPTER 2
Computer aided gene mining for gingerol biosynthesis

Inspite of the large body of genomic data obtained from the transcriptome of Zingiber officinale, very few studies have focused on the identification and characterization of miRNAs in gingerol biosynthesis. Zingiber officinale transcriptome was analyzed using EST dataset (38169 total) deposited in public domains. In this paper computational functional annotation of the available ESTs and identification of genes which play a significant role in gingerol biosynthesis are described. Zingiber officinale transcriptome was analyzed using EST dataset (38169 total) from ncbi. ESTs were clustered and assembled, resulting in 8624 contigs and 8821 singletons. Assembled dataset was then submitted to the EST functional annotation workflow including blast, gene ontology (go) analysis, and pathway enrichment by kyoto encyclopedia of genes and genomes (kegg) and interproscan. The unigene datasets were further exploited to identify simple sequence repeats that enable linkage mapping. A total of 409 simple sequence repeats were identified from the contigs. Furthermore we examined the existence of novel miRNAs from the ESTs in rhizome, root and leaf tissues. EST analysis revealed the presence of single hypothetical miRNA in rhizome tissue. The hypothetical miRNA is warranted to play an important role in controlling genes involved in gingerol biosynthesis and hence demands experimental validation. The assembly and associated information of transcriptome data provides a comprehensive functional and evolutionary characterization of genomics of Zingiber officinale. As an effort to make the genomic and transcriptomic data widely available to the public domain, the results were integrated into a web-based Ginger EST database which is freely accessible at http://www.kaubic. in/gingerest/.
Embryonic Signaling Pathways and Rhabdomyosarcoma: Contributions to Cancer Development and Opportunities for Therapeutic Targeting

Rhabdomyosarcoma is the most common soft tissue sarcoma of childhood and adolescence, accounting for approximately 7% of childhood cancers. Current therapies include nonspecific cytotoxic chemotherapy regimens, radiation therapy, and surgery; however, these multimodality strategies are unsuccessful in the majority of patients with high-risk disease. It is generally believed that these tumors represent arrested or aberrant skeletal muscle development, and, accordingly, developmental signaling pathways critical to myogenesis such as Notch, WNT, and Hedgehog may represent new therapeutic targets. In this paper, we summarize the current preclinical studies linking these embryonic pathways to rhabdomyosarcoma tumorigenesis and provide support for the investigation of targeted therapies in this embryonic cancer.
iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks

Mapping gene regulatory networks is a significant challenge in systems biology, yet only a few methods are currently capable of systems-level identification of transcription factors (TFs) that bind a specific regulatory element. We developed a microfluidic method for integrated systems-level interaction mapping of TF–DNA interactions, generating and interrogating an array of 423 full-length Drosophila TFs. With integrated systems-level interaction mapping, it is now possible to rapidly and quantitatively map gene regulatory networks of higher eukaryotes.
Prosodic phrasing and syntactic structure in Greek

This is a study of prosodic phrasing in relation to syntactic structure as a function of female and male speaker’s gender as well as normal and fast speech tempo in Greek. The results indicate: (1) prosodic phrasing has a 95% identification rate; (2) prosodic phrasing has a major effect on final tonal boundaries; (3) speech tempo has a major effect on pause productions but only a marginal effect on tonal productions; (4) speaker’s gender has a major effect on both tonal and pause productions.
A PAA-PSO technique for investment strategies in the financial market

Particle Swarm Optimization algorithm (PSO), when applied to problems with continuous variables, presents results with better quality at a lower computational cost when compared to the Genetic Algorithm (GA). Thus, the PSO becomes a very useful method to be applied with investment strategies used to optimize profit from operations made in the stock market, since investors seek quick and profitable results for their decision making. In this context, the Symbolic Aggregate Approximation (SAX) and Piecewise Aggregate Approximation (PAA) are time series representation techniques that, when used with optimization algorithms like PSO or GA, can help investors discover hidden and relevant patterns in financial time series data. The SAX uses discrete variables to represent their values, whereas PAA uses continuous values. Thus, this paper proposes the PAA-PSO technique, which combines the PAA with the optimization of PSO for discovery of patterns that will be used with a formulated investment strategy in order to maximize the profit from operations made in the stock market. Experiments that compare the proposed method to the results of the SAX-GA technique, which combines the techniques of SAX and GA in their investment strategy, are reported.
Flagellin polymerisation control by a cytosolic export chaperone.

Assembly of the long helical filament of the bacterial flagellum requires polymerisation of ca 20,000 flagellin (FliC) monomeric subunits into the growing structure extending from the cell surface. Here, we show that export of Salmonella flagellin is facilitated specifically by a cytosolic protein, FliS, and that FliS binds to the FliC C-terminal helical domain, which contributes to stabilisation of flagellin subunit interactions during polymerisation. Stable complexes of FliS with flagellin were assembled efficiently in vitro, apparently by FliS homodimers binding to FliC monomers. The data suggest that FliS acts as a substrate-specific chaperone, preventing premature interaction of newly synthesised flagellin subunits in the cytosol. Compatible with this view, FliS was able to prevent in vitro polymerisation of FliC into filaments.
An Embodied Approach to Understanding: Making Sense of the World Through Simulated Bodily Activity

Even though understanding is a very widely used concept, both colloquially and in scholarly work, its definition is nebulous and it is not well-studied as a psychological construct, compared to other psychological constructs like learning and memory. Studying understanding based on third-person (e.g., behavioral, neuroimaging) data alone presents unique challenges. Understanding refers to a first-person experience of making sense of an event or a conceptual domain, and therefore requires incorporation of multiple levels of study, at the first-person (phenomenological), behavioral, and neural levels. Previously, psychological understanding was defined as a form of conscious knowing. Alternatively, biofunctional approach extends to unconscious, implicit, automatic, and intuitive aspects of cognition. Here, to bridge these two approaches an embodied and evolutionary perspective is provided to situate biofunctional understanding in theories of embodiment, and to discuss how simulation theories of cognition, which regard simulation of sensorimotor and affective states as a central tenet of cognition, can bridge the gap between biofunctional and psychological understanding.
Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function

We have recently described a new conformational search strategy for protein folding algorithms called the CGU (convex global underestimator) method. Here we use a simplified protein chain representation and a differentiable form of the Sun/Thomas/Dill energy function to test the CGU method. Standard search methods, such as Monte Carlo and molecular dynamics are slowed by kinetic traps. That is, the computer time depends more strongly on the shape of the energy landscape (dictated by the amino acid sequence) than on the number of degrees of freedom (dictated by the chain length). The CGU method is not subject to this limitation, since it explores the underside of the energy landscape, not the top. We find that the CGU computer time is largely independent of the monomer sequence for different chain folds and scales as O(n4) with chain length. By using different starting points, we show that the method appears to find global minima. Since we can currently find stable states of 36-residue chains in 2.4 hours, the method may be practical for small proteins.
The Dystrophin Dp186 Isoform Regulates Neurotransmitter Release at a Central Synapse in Drosophila

The Dystrophin protein is encoded by a gene that, when mutated in humans, can cause Duchenne muscular dystrophy, a disease characterized by progressive muscle wasting. A number of Duchenne patients also exhibit poorly understood mental retardation, likely associated with loss of a brain-specific isoform. Furthermore, although Dystrophin isoforms and the related Utrophin protein have long been known to localize at synapses, their functions remain essentially unknown. In Drosophila, we find that the CNS-specific Dp186 isoform localizes to the embryonic and larval neuropiles, regions rich in synaptic contacts. In the absence of Dp186, evoked but not spontaneous presynaptic release is significantly enhanced. Increased presynaptic release can be fully rescued to wild-type levels by expression of a Dp186 transgene in the postsynaptic motoneuron, indicating that Dp186 likely regulates a retrograde signaling pathway. Potentiation of synaptic currents in the mutant also occurs when cholinergic transmission is inhibited or in the absence of Glass Bottom Boat (Gbb) or Wishful Thinking (Wit), a TGF-β ligand and receptor, respectively, both previously implicated in synaptic retrograde signaling. These results are consistent with the possibility that Dp186 modulates other non-Gbb/Wit-dependent retrograde signaling pathways required to maintain normal synaptic physiology.
Multi-Cloud: expectations and current approaches

Using resources and services from multiple Clouds is a natural evolution from consuming the ones from in-silo Clouds. Technological and administrative barriers are however slowing the process. Fortunately the recent years are marked by the appearance of several solutions that are partially overpassing them. However, the approaches are quite various and not adopted at large scale. This paper intends to offer a snapshot of the current state-of-the-art and to identify the future steps in building Multi-Clouds. A list of basic requirements for a Multi-Cloud is proposed.
PHD finger of autoimmune regulator: An epigenetic link between the histone modifications and tissue-specific antigen expression in thymus

Methylation of lysine residues on histone H3 tails regulates transcription. A recent addition to the list of known methylated histone binding modules is the plant homeodomain (PHD) finger, which is usually found in nuclear proteins with chromatin-related functions. Autoimmune regulator (AIRE) protein contains two PHD fingers and mutations in AIRE gene cause the monogenic disease autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). AIRE is expressed in thymic medullary epithelial cells where it promotes the expression of tissue-specific antigens. However the mechanism by which AIRE controls gene expression is currently unknown and the function of its domains, in particular of its PHD fingers is still elusive and controversial. In this review we discuss recent works on AIRE PHD finger(s) providing a new link between the status of histone modifications and the regulation of tissue-specific antigen expression in thymus.
Effect of Intracellular Magnesium and Oxygen Tension on K+-Cl- Cotransport in Normal and Sickle Human Red Cells

In red cells from normal individuals (HbA cells), the K+-Cl- cotransporter (KCC) is inactivated by low O2 tension whilst in those from sickle cell patients (HbS cells), it remains fully active. Changes in free intracellular [Mg2+] have been proposed as a mechanism. In HbA cells, KCC activity was stimulated by Mg2+ depletion and inhibited by Mg2+ loading but the effect of O2 was independent of Mg2+. At all [Mg2+]is, the transporter was stimulated in oxygenated cells, minimally active in deoxygenated ones. By contrast, the stimulatory effects of O2 was abolished by inhibitors of protein (de)phosphorylation. HbS cells had elevated KCC activity, which was of similar magnitude in oxygenated and deoxygenated cells, regardless of Mg2+ clamping. In deoxygenated cells, the antisickling agent dimethyl adipimidate inhibited sickling, Psickle and KCC. Results indicate a role for protein phosphorylation in O2 dependence of KCC, with different activities of the relevant enzymes in HbA and HbS cells, probably dependent on Hb