Miracle-dz/UniFAR-FTUs huggingface dataset:
The PDZ Protein Canoe/AF-6 Links Ras-MAPK, Notch and Wingless/Wnt Signaling Pathways by Directly Interacting with Ras, Notch and Dishevelled

Over the past few years, it has become increasingly apparent that signal transduction pathways are not merely linear cascades; they are organized into complex signaling networks that require high levels of regulation to generate precise and unique cell responses. However, the underlying regulatory mechanisms by which signaling pathways cross-communicate remain poorly understood. Here we show that the Ras-binding protein Canoe (Cno)/AF-6, a PDZ protein normally associated with cellular junctions, is a key modulator of Wingless (Wg)/Wnt, Ras-Mitogen Activated Protein Kinase (MAPK) and Notch (N) signaling pathways cross-communication. Our data show a repressive effect of Cno/AF-6 on these three signaling pathways through physical interactions with Ras, N and the cytoplasmic protein Dishevelled (Dsh), a key Wg effector. We propose a model in which Cno, through those interactions, actively coordinates, at the membrane level, Ras-MAPK, N and Wg signaling pathways during progenitor specification.
The Karyotype of the Yellow Dung Fly, Scathophaga stercoraria, a Model Organism in Studies of Sexual Selection

Abstract Knowledge of karyotypical characteristics of a species is essential for understanding how sexually selected and sexually antagonistic traits evolve. The yellow dung fly Scathophaga stercoraria L. (Diptera: Scathophagidae) is an established model system for studies of sexual selection and sexual conflict, but karyotypical data are lacking to date. Here, the karyotype of S. stercoraria was characterized using conventional Giemsa-staining and C-banding techniques. The diploid chromosome set consists of 6 pairs of bi-armed meta- or submetacentric chromosomes. The sex chromosomes are the largest chromosomes and constitute 30% of the total length of the diploid set in females and about 25% in males. Males are the heterogametic sex, and the length of the Y chromosome is about three-quarters of that of the X chromosome. C-banding revealed that both sex chromosomes are largely heterochromatic. In contrast, in the five autosome pairs, heterochromatin is limited to narrow bands in the centromeric regions. This karyotypic information will help provide a more profound understanding of the inheritance of phenotypic variation in reproductive traits and the chromosomal locations of underlying genes.
Calibration of head-mounted displays for augmented reality applications

The authors have developed "augmented reality" technology, consisting of a see-through head-mounted display, a robust, accurate position/orientation sensor, and their supporting electronics and software. Their primary goal is to apply this technology to touch labor manufacturing processes, enabling a factory worker to view index markings or instructions as if they were painted on the surface of a workpiece. In order to accurately project graphics onto specific points of a workpiece, it is necessary to have the coordinates of the workpiece, the display's virtual screen, the position sensor, and the user's eyes in the same coordinate system. The linear transformation and projection of each point to be displayed from world coordinates to virtual screen coordinates are described, and the experimental procedures for determining the correct values of the calibration parameters are characterized. <<ETX>>
New Approaches for Virtual Private Network Design

Virtual private network design is the following NP-hard problem. We are given a communication network, represented as a weighted graph with thresholds on the nodes which represent the amount of flow that a node can send to and receive from the network. The task is to reserve capacities at minimum cost and to specify paths between every ordered pair of nodes such that all valid traffic-matrices can be routed along the corresponding paths. Recently, this network design problem has received considerable attention in the literature. It is motivated by the fact that the exact amount of flow which is exchanged between terminals is not known in advance and prediction is often illusive. The main contributions of this paper are as follows:Using Hu’s 2-commodity flow theorem, we provide a new lower bound on the cost of an optimum solution. Using this lower bound we reanalyze a simple routing scheme which has been described in the literature many times and provide a considerably stronger upper bound on its approximation ratio. We present a new randomized approximation algorithm for which, in contrast to earlier approaches from the literature, the resulting solution does not have tree structure. Finally we show that a combination of our new algorithm with the simple routing scheme yields a randomized algorithm with expected performance ratio 3.55 for virtual private network design. This is a considerable improvement of the previously best known approximation results (5.55 STOC’03, 4.74 SODA’05).
Energy-aware register file re-partitioning for clustered VLIW architectures

VLIW architectures have gained acceptance in embedded systems. Traditional monolithic register file is not suitable for VLIW architectures with a large number of functional units. Clustered VLIW architecture is often applied, where the register file is partitioned into a number of smaller register files. Register files represent a substantial portion of the energy consumption in modern processors, and it is growing rapidly with wider instruction width. Most of the known clustered VLIW architectures partition the register file evenly among clusters. In this paper, we study the effect of energy consumption with register file re-partitioning on clustered VLIW architecture, where register files are not necessarily partitioned evenly. We present algorithms to compute energy-efficient re-partition of register files under different conditions. The impact of different intercluster communication models as well as the impact of program behavior on the register file re-partitioning are analyzed in this paper. Experimental results show that energy saving can be achieved using the proposed techniques.
Delta vector taylor series environment compensation for speaker recognition

The performance of speaker recognition algorithms drops signi(cid:12)cantly when testing and training acoustic environments di(cid:11)er. This decrease is caused by the statistical mismatch between the statistics representing the speaker and the testing acoustic data. This paper reports our preliminary results on the application of a novel environmental compensation algorithm to the problem of speaker recognition and identi(cid:12)cation. This new technique, called the Delta Vector Taylor Series (DVTS) approach, improves performance at signal-to-noise ratios below 20dB. The algorithm imposes a model of how the environment modi(cid:12)es speaker statistics and uses Expectation-Maximization (EM) to solve a joint maximum likelihood formulation for the speaker recognition problem over both the speakers and the environment. We report experi-mental results on a subset of the TIMIT and NTIMIT database.
Measuring and modelling Internet diffusion using second level domains: the case of Italy

The last 10 years witnessed an exponential growth of the Internet. According to Hobbes' Internet Timeline, the Internet hosts are about 93 million, while in 1989 they were 100,000. The same happens for second level domain names. In July 1989 the registered domains were about 3,900 while they were over 2 million in July 2000. This paper reports about the construction of a database containing daily observations on registrations of second level domain names underneath the it ccTLD in order to analyse the diffusion of Internet among families and businesses. The section of the database referring to domains registered by individuals is analysed. The penetration rate over the relevant population of potential adopters is computed at highly disaggregated geographical level (province). A concentration analysis is carried out to investigate whether the geographical distribution of Internet is less concentrated than population and income suggesting a diffusive effect. Regression analysis is carried out using demographic, social, economic and infrastructure indicators. Finally we briefly describe the further developments of our research. At the present we are constructing a database containing domains registered by firms together with data about the registrants; the idea is to use this new database and the previous one in order to check for the existence of power laws both in the number of domains registered in each province and in the number of domains registered by each firm.
Subspace identification method incorporated with a priori information characterized in frequency domain

We propose a subspace identification method that involves a priori information of the system characterized in the frequency domain. Some properties of the system over all frequency range are transformed into matrix inequalities that are linear in system matrices, by using the well-known Kalman-Yakubovich-Popov (KYP) lemma. To construct a model that represents the specified frequency characteristics, we formulate a subspace identification problem under the matrix inequality constraints. This constrained problem is in a class of nonlinear optimization problems, then we reduce it to a convex one by applying a proper transformation. Furthermore, the proposed method is extended to that incorporated with a priori information characterized only in a certain frequency range. Finally, we verify the effectiveness of the proposed method in a numerical simulation.
Time-frequency filtering applied to terahertz time-domain spectroscopy

We introduce the use of Time-Frequency (TF) filtering applied to Terahertz Time-Domain Spectroscopy (THz-TDS) data in order to extract valuable information hidden into the noise floor. The Short Time Fourier Transform (STFT) provides a spectrum analysis in time, we optimized its Gaussian window in order to analyse and filter the THz signals of substances. The formalism presented allows an efficient denoising of THz-TDS data which could prove useful during the investigation of highly absorbing samples.
Osteoblastic differentiation and P-glycoprotein multidrug resistance in a murine osteosarcoma model

A recent study of multidrug resistance (MDR) 1 gene transfected osteosarcoma cells found a cause-effect relationship between increased expression of P-glycoprotein (P-gp) and a low aggressive phenotype. However, several experimental and clinical studies have observed contradictory findings in that P-gp expression has been associated with tumour progression. In the present study, we characterized P-gp-positive and P-gp-negative single-cell clones of a murine osteosarcoma, to further investigate the relationship between P-gp expression and changes in cell phenotype. Although these clones were all selected by doxorubicin (DOX) exposure, they were heterogeneous with respect to MDR1 gene expression. The P-gp-positive clones revealed MDR phenotype, whereas the P-gp-negative clones showed no resistance to drugs. Morphological and functional analysis showed that both the P-gp-positive and P-gp-negative clones were more differentiated than the parent cells in terms of enhanced activity of cellular alkaline phosphatase, an increase in well-organized actin stress fibres and enhanced osteogenic activity. Moreover, these subclones all displayed a decrease in malignant potential such as oncogenic activity, tumour growth rate and metastatic ability, regardless of their P-gp status. These results indicate that the observed osteoblastic differentiation and less aggressive phenotype in DOX-selected osteosarcoma cells may not only be explained by the direct effect of P-gp, and accordingly, consideration of the effect of DOX, as well as P-gp, appears to be important. © 2000 Cancer Research Campaign
Metric-based vs peer-reviewed evaluation of a research output: Lesson learnt from UK’s national research assessment exercise

Purpose There is a general inquisition regarding the monetary value of a research output, as a substantial amount of funding in modern academia is essentially awarded to good research presented in the form of journal articles, conferences papers, performances, compositions, exhibitions, books and book chapters etc., which, eventually leads to another question if the value varies across different disciplines. Answers to these questions will not only assist academics and researchers, but will also help higher education institutions (HEIs) make informed decisions in their administrative and research policies. Design and methodology To examine both the questions, we applied the United Kingdom’s recently concluded national research assessment exercise known as the Research Excellence Framework (REF) 2014 as a case study. All the data for this study is sourced from the openly available publications which arose from the digital repositories of REF’s results and HEFCE’s funding allocations. Findings A world leading output earns between £7504 and £14,639 per year within the REF cycle, whereas an internationally excellent output earns between £1876 and £3659, varying according to their area of research. Secondly, an investigation into the impact rating of 25315 journal articles submitted in five areas of research by UK HEIs and their awarded funding revealed a linear relationship between the percentage of quartile-one journal publications and percentage of 4* outputs in Clinical Medicine, Physics and Psychology/Psychiatry/Neuroscience UoAs, and no relationship was found in the Classics and Anthropology/Development Studies UoAs, due to the fact that most publications in the latter two disciplines are not journal articles. Practical implications The findings provide an indication of the monetary value of a research output, from the perspectives of government funding for research, and also what makes a good output, i.e. whether a relationship exists between good quality output and the source of its publication. The findings may also influence future REF submission strategies in HEIs and ascertain that the impact rating of the journals is not necessarily a reflection of the quality of research in every discipline, and this may have a significant influence on the future of scholarly communications in general. Originality According to the author’s knowledge, this is the first time an investigation has estimated the monetary value of a good research output.
Neurodevelopment of children exposed in utero to lamotrigine, sodium valproate and carbamazepine

Objective To establish the relative risks of in utero exposure to lamotrigine (LTG), sodium valproate (NaV) and carbamazepine (CBZ) monotherapy for neurodevelopment. Design Observational cohort study. Patients and methods The study group consisted of children in Northern Ireland aged 9–60 months born to mothers who had enrolled with the UK Epilepsy and Pregnancy Register. The control group consisted of children identified from the Child Health System database across Northern Ireland. Data were gathered on covariates recognised as influencing child development. Main outcome measures Neurodevelopment assessed using either the Bayley Scales of Infant Development or the Griffiths Mental Development Scales. Results 210 children underwent assessment by a single researcher blinded to antiepileptic drug exposure. 23 (39.6%) children exposed in utero to NaV, 10 (20.4%) exposed to CBZ and one (2.9%) exposed to LTG had evidence of mild or significant developmental delay, compared to two (4.5%) children in the control group. Multivariable analysis demonstrated that in utero exposure to NaV (OR 26.1, 95% CI 4.9 to 139; p<0.001) and to CBZ (OR 7.7, 95% CI 1.4 to 43.1; p<0.01) but not to LTG had a significant detrimental effect on neurodevelopment. Conclusion In utero exposure to LTG did not have the detrimental effect on child development that was seen with NaV and with CBZ.
A Rotation Test to Verify Latent Structure

In multivariate regression models we have the opportunity to look for hidden structure unrelated to the observed predictors. However, when one fits a model involving such latent variables it is important to be able to tell if the structure is real, or just an artifact of correlation in the regression errors. We develop a new statistical test based on random rotations for verifying the existence of latent variables. The rotations are carefully constructed to rotate orthogonally to the column space of the regression model. We find that only non-Gaussian latent variables are detectable, a finding that parallels a well known phenomenon in independent components analysis. We base our test on a measure of non-Gaussianity in the histogram of the principal eigenvector components instead of on the eigenvalue. The method finds and verifies some latent dichotomies in the microarray data from the AGEMAP consortium.
Construction and Application of a Protein Interaction Map for White Spot Syndrome Virus (WSSV)*

White spot syndrome virus (WSSV) is currently the most serious global threat for cultured shrimp production. Although its large, double-stranded DNA genome has been completely characterized, most putative protein functions remain obscure. To provide more informative knowledge about this virus, a proteomic-scale network of WSSV-WSSV protein interactions was carried out using a comprehensive yeast two-hybrid analysis. An array of yeast transformants containing each WSSV open reading frame fused with GAL4 DNA binding domain and GAL4 activation domain was constructed yielding 187 bait and 182 prey constructs, respectively. On screening of ∼28,000 pairwise combinations, 710 interactions were obtained from 143 baits. An independent coimmunoprecipitation assay (co-IP) was performed to validate the selected protein interaction pairs identified from the yeast two-hybrid approach. The program Cytoscape was employed to create a WSSV protein–protein interaction (PPI) network. The topology of the WSSV PPI network was based on the Barabási-Albert model and consisted of a scale-free network that resembled other established viral protein interaction networks. Using the RNA interference approach, knocking down either of two candidate hub proteins gave shrimp more protection against WSSV than knocking down a nonhub gene. The WSSV protein interaction map established in this study provides novel guidance for further studies on shrimp viral pathogenesis, host-viral protein interaction and potential targets for therapeutic and preventative antiviral strategies in shrimp aquaculture.
Purification and Characterization of a Novel Recombinant Highly Enantioselective Short-Chain NAD(H)-Dependent Alcohol Dehydrogenase from Thermus thermophilus

ABSTRACT The gene encoding a novel alcohol dehydrogenase (ADH) that belongs to the short-chain dehydrogenase/reductase (SDR) superfamily was identified in the extremely thermophilic, halotolerant gram-negative eubacterium Thermus thermophilus HB27. The T. thermophilus ADH gene (adhTt) was heterologously overexpressed in Escherichia coli, and the protein (ADHTt) was purified to homogeneity and characterized. ADHTt is a tetrameric enzyme consisting of identical 26,961-Da subunits composed of 256 amino acids. The enzyme has remarkable thermophilicity and thermal stability, displaying activity at temperatures up to ∼73°C and a 30-min half-inactivation temperature of ∼90°C, as well as good tolerance to common organic solvents. ADHTt has a strict requirement for NAD(H) as the coenzyme, a preference for reduction of aromatic ketones and α-keto esters, and poor activity on aromatic alcohols and aldehydes. This thermophilic enzyme catalyzes the following reactions with Prelog specificity: the reduction of acetophenone, 2,2,2-trifluoroacetophenone, α-tetralone, and α-methyl and α-ethyl benzoylformates to (S)-(−)-1-phenylethanol (>99% enantiomeric excess [ee]), (R)-α-(trifluoromethyl)benzyl alcohol (93% ee), (S)-α-tetralol (>99% ee), methyl (R)-(−)-mandelate (92% ee), and ethyl (R)-(−)-mandelate (95% ee), respectively, by way of an efficient in situ NADH-recycling system involving 2-propanol and a second thermophilic ADH. This study further supports the critical role of the D37 residue in discriminating NAD(H) from NADP(H) in members of the SDR superfamily.
Les circuits neuronaux de l'aversion olfactive conditionnée : approche électrophysiologique chez le rat vigile

L’objectif de cette these est de decrire le reseau cerebral et la dynamique neuronale qui pourraient servir de support aux aversions alimentaires de type olfactives. Nous avons realise des enregistrements multisites de potentiel de champ locaux chez le rat vigile engage dans cet apprentissage, en proposant deux modes de presentation de l’indice olfactif : a proximite de l’eau de boisson (distal) ou ingere (distal-proximal). Apres apprentissage, la presentation du seul indice distal induit l’emergence d’une activite oscillatoire de forte amplitude dans la bande de frequence beta (15-40 Hz). Finement correlee au comportement d’aversion de l’animal, cette activite est proposee comme la signature du reseau de structures fonctionnellement impliquees dans la reconnaissance de l’odeur en tant que signal. Nous montrons que ce reseau peut etre plus ou moins etendu selon la facon dont le stimulus a ete percu lors du conditionnement: dans certaines aires (bulbe olfactif, cortex piriforme, amygdale basolaterale, cortex orbitofrontal) la modulation en puissance de l’activite beta se fait independamment du mode de conditionnement; dans d’autres aires (cortex insulaire, cortex infralimbique) ces changements ont lieu si et seulement si l’odeur a ete ingeree. Completes par l’etude des interactions fonctionnelles entre ces differentes structures dans la bande de frequence consideree, ces resultats nous permettent de mieux comprendre comment un stimulus peut etre represente en memoire dans un reseau cerebral en fonction de l’experience que l’animal en a fait.
A Wearable Inertial Measurement Unit for Long-Term Monitoring in the Dependency Care Area

Human movement analysis is a field of wide interest since it enables the assessment of a large variety of variables related to quality of life. Human movement can be accurately evaluated through Inertial Measurement Units (IMU), which are wearable and comfortable devices with long battery life. The IMU's movement signals might be, on the one hand, stored in a digital support, in which an analysis is performed a posteriori. On the other hand, the signal analysis might take place in the same IMU at the same time as the signal acquisition through online classifiers. The new sensor system presented in this paper is designed for both collecting movement signals and analyzing them in real-time. This system is a flexible platform useful for collecting data via a triaxial accelerometer, a gyroscope and a magnetometer, with the possibility to incorporate other information sources in real-time. A μSD card can store all inertial data and a Bluetooth module is able to send information to other external devices and receive data from other sources. The system presented is being used in the real-time detection and analysis of Parkinson's disease symptoms, in gait analysis, and in a fall detection system.