A diphtheria toxin resistance marker for in vitro and in vivo selection of stably transduced human cells

We developed a selectable marker rendering human cells resistant to Diphtheria Toxin (DT). The marker (DT(R)) consists of a primary microRNA sequence engineered to downregulate the ubiquitous DPH2 gene, a key enzyme for the biosynthesis of the DT target diphthamide. DT(R) expression in human cells invariably rendered them resistant to DT in vitro, without altering basal cell growth. DT(R)-based selection efficiency and stability were comparable to those of established drug-resistance markers. As mice are insensitive to DT, DT(R)-based selection can be also applied in vivo. Direct injection of a GFP-DT(R) lentiviral vector into human cancer cell-line xenografts and patient-derived tumorgrafts implanted in mice, followed by systemic DT administration, yielded tumors entirely composed of permanently transduced cells and detectable by imaging systems. This approach enabled high-efficiency in vivo selection of xenografted human tumor tissues expressing ectopic transgenes, a hitherto unmet need for functional and morphological studies in laboratory animals

The Critical Properties of Two-dimensional Oscillator Arrays

We present a renormalization group study of two dimensional arrays of oscillators, with dissipative, short range interactions. We consider the case of non-identical oscillators, with distributed intrinsic frequencies within the array and study the steady-state properties of the system. In two dimensions no macroscopic mutual entrainment is found but, for identical oscillators, critical behavior of the Berezinskii-Kosterlitz-Thouless type is shown to be present. We then discuss the stability of (BKT) order in the physical case of distributed quenched random frequencies. In order to do that, we show how the steady-state dynamical properties of the two dimensional array of non-identical oscillators are related to the equilibrium properties of the XY model with quenched randomness, that has been already studied in the past. We propose a novel set of recursion relations to study this system within the Migdal Kadanoff renormalization group scheme, by mean of the discrete clock-state formulation. We compute the phase diagram in the presence of random dissipative coupling, at finite values of the clock state parameter. Possible experimental applications in two dimensional arrays of microelectromechanical oscillators are briefly suggested.Comment: Contribution to the conference "Viewing the World through Spin Glasses" in honour of Professor David Sherrington on the occasion of his 65th birthda

Otter-Knowledge: benchmarks of multimodal knowledge graph representation learning from different sources for drug discovery

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning

Transcriptional Hallmarks of Noonan Syndrome and Noonan-Like Syndrome with Loose Anagen Hair

Noonan syndrome (NS) is among the most common nonchromosomal disorders affecting development and growth. NS is genetically heterogeneous, being caused by germline mutations affecting various genes implicated in the RAS signaling network. This network transduces extracellular signals into intracellular biochemical and transcriptional responses controlling cell proliferation, differentiation, metabolism, and senescence. To explore the transcriptional consequences of NS-causing mutations, we performed global mRNA expression profiling on peripheral blood mononuclear cells obtained from 23 NS patients carrying heterozygous mutations in PTPN11 or SOS1. Gene expression profiling was also resolved in five subjects with Noonan-like syndrome with loose anagen hair (NS/LAH), a condition clinically related to NS and caused by an invariant mutation in SHOC2. Robust transcriptional signatures were found to specifically discriminate each of the three mutation groups from 21 age- and sex-matched controls. Despite the only partial overlap in terms of gene composition, the three signatures showed a notable concordance in terms of biological processes and regulatory circuits affected. These data establish expression profiling of peripheral blood mononuclear cells as a powerful tool to appreciate differential perturbations driven by germline mutations of transducers involved in RAS signaling and to dissect molecular mechanisms underlying NS and other RASopathies. Hum Mutat 33:703–709, 2012. © 2012 Wiley Periodicals, Inc

The RNA-binding protein ESRP1 promotes human colorectal cancer progression

Epithelial splicing regulatory protein 1 (ESRP1) is an epithelial cell-specific RNA binding protein that controls several key cellular processes, like alternative splicing and translation. Previous studies have demonstrated a tumor suppressor role for this protein. Recently, however, a pro-metastatic function of ESRP1 has been reported. We thus aimed at clarifying the role of ESRP1 in Colorectal Cancer (CRC) by performing loss- and gain-of-function studies, and evaluating tumorigenesis and malignancy with in vitro and in vivo approaches. We found that ESRP1 plays a role in anchorage-independent growth of CRC cells. ESRP1-overexpressing cells grown in suspension showed enhanced fibroblast growth factor receptor (FGFR1/2) signalling, Akt activation, and Snail upregulation. Moreover, ESRP1 promoted the ability of CRC cells to generate macrometastases in mice livers. High ESRP1 expression may thus stimulate growth of cancer epithelial cells and promote colorectal cancer progression. Our findings provide mechanistic insights into a previously unreported, pro-oncogenic role for ESRP1 in CRC, and suggest that fine-tuning the level of this RNA-binding protein could be relevant in modulating tumor growth in a subset of CRC patients

Type I interferon-mediated autoinflammation due to DNase II deficiency

Microbial nucleic acid recognition serves as the major stimulus to an antiviral response, implying a requirement to limit the misrepresentation of self nucleic acids as non-self and the induction of autoinflammation. By systematic screening using a panel of interferon-stimulated genes we identify two siblings and a singleton variably demonstrating severe neonatal anemia, membranoproliferative glomerulonephritis, liver fibrosis, deforming arthropathy and increased anti-DNA antibodies. In both families we identify biallelic mutations in DNASE2, associated with a loss of DNase II endonuclease activity. We record increased interferon alpha protein levels using digital ELISA, enhanced interferon signaling by RNA-Seq analysis and constitutive upregulation of phosphorylated STAT1 and STAT3 in patient lymphocytes and monocytes. A hematological disease transcriptomic signature and increased numbers of erythroblasts are recorded in patient peripheral blood, suggesting that interferon might have a particular effect on hematopoiesis. These data define a type I interferonopathy due to DNase II deficiency in humans

The Opportunity Costs of Public Funds Concepts and Issues

This paper reviews the main conceptual issues regarding the notion of Opportunity Cost of Public Funds (OCPF) and its use in normative economics. This notion occupies only a marginal and sometimes anecdotal role in the public economic literature and appears to be too often used without the definitional unambiguousness that would make it helpful for economic analysis. This situation is unsatisfactory considering the importance of (some of) the mechanisms described by the concept and the magnitude of these effects that are such as to heavily impact any budgetary practice. We find that among the mechanisms that economists call "opportunity costs" the deadweight loss and, to a lesser extent, administrative costs seem to be the most relevant, whereas the impact of the crowding out is more discussible. We also analyze how the question of opportunity costs is contingent upon some hypothesis about the financing mechanism of the public expenditures and we suggest that the most likely situation is the one where public expenses are financed through the eviction of other alternative uses of the public funding. We also provide a review of available quantifications and recommendations to the practitioners

IOM - Internet of mobility: A wearable device for outdoor data collection

Current technology allows the collection of data about cities by communities collaborating for the wellbeing of the city. The solution described in this paper is a wearable device ecosystem, called IOM (Internet of Mobility), consisting of a wearable device collecting environmental data through sensors to be visualized on a mobile or web platform. The paper focuses on the requirements analysis involving different types of target users and on the design of the wearable device