Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus

Background During the last years the quantification of immune response under immunological challenges, e.g. parasitation, has been a major focus of research. In this context, the expression of immune response genes in teleost fish has been surveyed for scientific and commercial purposes. Despite the fact that it was shown in teleostei and other taxa that the gene for beta-actin is not the most stably expressed housekeeping gene (HKG), depending on the tissue and experimental treatment, the gene has been us Results To establish a reliable method for the measurement of immune gene expression in Gasterosteus aculeatus, sequences from the now available genome database and an EST library of the same species were used to select oligonucleotide primers for HKG, in order to perform quantitative reverse-transcription (RT) PCR. The expression stability of ten candidate reference genes was evaluated in three different tissues, and in five parasite treatment groups, using the three algorithms BestKeeper, geNorm and N Conclusion As they were the most stably expressed genes in all tissues examined, we suggest using the genes for the L13a ribosomal binding protein and ubiquitin as alternative or additional reference genes in expression analysis in Gasterosteus aculeatus.

What two models may teach us about duality violations in QCD

Though the operator product expansion is applicable in the calculation of current correlation functions in the Euclidean region, when approaching the Minkowskian domain, violations of quark-hadron duality are expected to occur, due to the presence of bound-state or resonance poles. In QCD finite-energy sum rules, contour integrals in the complex energy plane down to the Minkowskian axis have to be performed, and thus the question arises what the impact of duality violations may be. The structure and possible relevance of duality violations is investigated on the basis of two models: the Coulomb system and a model for light-quark correlators which has already been studied previously. As might yet be naively expected, duality violations are in some sense "maximal" for zero-width bound states and they become weaker for broader resonances whose poles lie further away from the physical axis. Furthermore, to a certain extent, they can be suppressed by choosing appropriate weight functions in the finite-energy sum rules. A simplified Ansatz for including effects of duality violations in phenomenological QCD sum rule analyses is discussed as well.Comment: 17 pages, 6 figures; version to appear in JHE

Language Identification in Short Utterances Using Long Short-Term Memory (LSTM) Recurrent Neural Networks

Zazo R, Lozano-Diez A, Gonzalez-Dominguez J, T. Toledano D, Gonzalez-Rodriguez J (2016) Language Identification in Short Utterances Using Long Short-Term Memory (LSTM) Recurrent Neural Networks. PLoS ONE 11(1): e0146917. doi:10.1371/journal.pone.0146917Long Short Term Memory (LSTM) Recurrent Neural Networks (RNNs) have recently outperformed other state-of-the-art approaches, such as i-vector and Deep Neural Networks (DNNs), in automatic Language Identification (LID), particularly when dealing with very short utterances (similar to 3s). In this contribution we present an open-source, end-to-end, LSTM RNN system running on limited computational resources (a single GPU) that outperforms a reference i-vector system on a subset of the NIST Language Recognition Evaluation (8 target languages, 3s task) by up to a 26%. This result is in line with previously published research using proprietary LSTM implementations and huge computational resources, which made these former results hardly reproducible. Further, we extend those previous experiments modeling unseen languages (out of set, OOS, modeling), which is crucial in real applications. Results show that a LSTM RNN with OOS modeling is able to detect these languages and generalizes robustly to unseen OOS languages. Finally, we also analyze the effect of even more limited test data (from 2.25s to 0.1s) proving that with as little as 0.5s an accuracy of over 50% can be achieved.This work has been supported by project CMC-V2: Caracterizacion, Modelado y Compensacion de Variabilidad en la Señal de Voz (TEC2012-37585-C02-01), funded by Ministerio de Economia y Competitividad, Spain

Electrophysiological Heterogeneity of Fast-Spiking Interneurons: Chandelier versus Basket Cells

In the prefrontal cortex, parvalbumin-positive inhibitory neurons play a prominent role in the neural circuitry that subserves working memory, and alterations in these neurons contribute to the pathophysiology of schizophrenia. Two morphologically distinct classes of parvalbumin neurons that target the perisomatic region of pyramidal neurons, chandelier cells (ChCs) and basket cells (BCs), are generally thought to have the same "fast-spiking" phenotype, which is characterized by a short action potential and high frequency firing without adaptation. However, findings from studies in different species suggest that certain electrophysiological membrane properties might differ between these two cell classes. In this study, we assessed the physiological heterogeneity of fast-spiking interneurons as a function of two factors: species (macaque monkey vs. rat) and morphology (chandelier vs. basket). We showed previously that electrophysiological membrane properties of BCs differ between these two species. Here, for the first time, we report differences in ChCs membrane properties between monkey and rat. We also found that a number of membrane properties differentiate ChCs from BCs. Some of these differences were species-independent (e.g., fast and medium afterhyperpolarization, firing frequency, and depolarizing sag), whereas the differences in the first spike latency between ChCs and BCs were species-specific. Our findings indicate that different combinations of electrophysiological membrane properties distinguish ChCs from BCs in rodents and primates. Such electrophysiological differences between ChCs and BCs likely contribute to their distinctive roles in cortical circuitry in each species. © 2013 Povysheva et al

Active Tension Network model suggests an exotic mechanical state realized in epithelial tissues.

Mechanical interactions play a crucial role in epithelial morphogenesis, yet understanding the complex mechanisms through which stress and deformation affect cell behavior remains an open problem. Here we formulate and analyze the Active Tension Network (ATN) model, which assumes that the mechanical balance of cells within a tissue is dominated by cortical tension and introduces tension-dependent active remodeling of the cortex. We find that ATNs exhibit unusual mechanical properties. Specifically, an ATN behaves as a fluid at short times, but at long times supports external tension like a solid. Furthermore, an ATN has an extensively degenerate equilibrium mechanical state associated with a discrete conformal - "isogonal" - deformation of cells. The ATN model predicts a constraint on equilibrium cell geometries, which we demonstrate to approximately hold in certain epithelial tissues. We further show that isogonal modes are observed in the fruit y embryo, accounting for the striking variability of apical areas of ventral cells and helping understand the early phase of gastrulation. Living matter realizes new and exotic mechanical states, the study of which helps to understand biological phenomena

Prognostic significance of lymphangiogenesis in pharyngolaryngeal carcinoma patients

<p>Abstract</p> <p>Background</p> <p>Lymphatic vessel spread is considered a major route for head and neck squamous cell carcinoma metastasis. Formation of new lymphatic vessels could facilitate the process, raising the malignant potential of these tumours. Recent identification of lymphatic markers allows the study of the lymphangiogenesis phenomenon. We searched for molecular events involved in the lymphangiogenic process that could have prognostic value in laryngeal/pharyngeal carcinoma patients.</p> <p>Methods</p> <p>104 paraffin-embedded pharyngeal/laryngeal tumour samples were studied. Immunohistochemical analysis of podoplanin and double immunofluorescence analysis of Ki-67 and D2-40 were performed. Lymph vessel density (inside the tumour mass, at its periphery or considered as a whole) and the presence of tumour emboli inside lymphatics were recorded. The proliferative state of endothelial lymphatic cells was evaluated.</p> <p>Results</p> <p>Lymphatic vessels were detected inside the tumour mass (75%) and in the surrounding tissue (80%); some of them in a proliferative state. Tumour emboli were detected in a high proportion of the cases (45%). Lymphatic vessel density was higher in the pharyngeal cases (p = 0.0029), in greater size (p = 0.039), more advanced stage primary tumours (p = 0.006) and in carcinomas of patients with affected nodes (p = 0.019). The presence of tumour emboli and a high global vessel density were indicators of poor prognosis (recorded as death from tumour) in the laryngeal group (p = 0.015 and p = 0.027, respectively), but notably not in the pharyngeal one. Interestingly, high global vessel density showed a negative prognostic value among pathologically staged N0 laryngeal carcinomas (p = 0.03).</p> <p>Conclusions</p> <p>The lymphangiogenic process correlated with aggressive tumour features (pN category, tumour size, tumour stage), but might play different roles in tumours arising from different anatomic sites.</p> <p>Our results suggest that detection of tumour emboli and assessment of global vessel density using the D2-40 antibody, may be useful in the clinical practice, as predictors of reduced survival among pN0 laryngeal carcinoma patients.</p