Miracle-dz/UniFAR-FTUs huggingface dataset:
Acute Disruption of the NMDA Receptor Subunit NR1 in the Honeybee Brain Selectively Impairs Memory Formation

Memory formation is a continuous process composed of multiple phases that can develop independently from each other. These phases depend on signaling pathways initiated after the activation of receptors in different brain regions. The NMDA receptor acts as a sensor of coincident activity between neural inputs, and, as such, its activation during learning is thought to be crucial for various forms of memory. In this study, we inhibited the expression of the NR1 subunit of the NMDA receptor in the honeybee brain using RNA interference. We show that the disruption of the subunit expression in the mushroom body region of the honeybee brain during and shortly after appetitive learning selectively impaired memory. Although the formation of mid-term memory and early long-term memory was impaired, late long-term memory was left intact. This indicates that late long-term memory formation differs in its dependence on NMDA receptor activity from earlier memory phases.
Multi-Block Bipartite Graph for Integrative Genomic Analysis

Human diseases involve a sequence of complex interactions between multiple biological processes. In particular, multiple genomic data such as Single Nucleotide Polymorphism (SNP), Copy Number Variation (CNV), DNA Methylation (DM), and their interactions simultaneously play an important role in human diseases. However, despite the widely known complex multi-layer biological processes and increased availability of the heterogeneous genomic data, most research has considered only a single type of genomic data. Furthermore, recent integrative genomic studies for the multiple genomic data have also been facing difficulties due to the high-dimensionality and complexity, especially when considering their intra- and inter-block interactions. In this paper, we introduce a novel multi-block bipartite graph and its inference methods, MB2I and sMB2I, for the integrative genomic study. The proposed methods not only integrate multiple genomic data but also incorporate intra/inter-block interactions by using a multi-block bipartite graph. In addition, the methods can be used to predict quantitative traits (e.g., gene expression, survival time) from the multi-block genomic data. The performance was assessed by simulation experiments that implement practical situations. We also applied the method to the human brain data of psychiatric disorders. The experimental results were analyzed by maximum edge biclique and biclustering, and biological findings were discussed.
Cell-autonomous Notch activity maintains the temporal specification potential of skeletal muscle stem cells

During organogenesis, a continuum of founder stem cells produces temporally distinct progeny until development is complete. Similarly, in skeletal myogenesis, phenotypically and functionally distinct myoblasts and differentiated cells are generated during development. How this occurs in muscle and other tissues in vertebrates remains largely unclear. We showed previously that committed cells are required for maintaining muscle stem cells. Here we show that active Notch signalling specifies a subpopulation of myogenic cells with high Pax7 expression. By genetically modulating Notch activity, we demonstrate that activated Notch (NICD) blocks terminal differentiation in an Rbpj-dependent manner that is sufficient to sustain stem/progenitor cells throughout embryogenesis, despite the absence of committed progeny. Although arrested in lineage progression, NICD-expressing cells of embryonic origin progressively mature and adopt characteristics of foetal myogenic cells, including expression of the foetal myogenesis regulator Nfix. siRNA-mediated silencing of NICD promotes the temporally appropriate foetal myogenic fate in spite of expression of markers for multiple cell types. We uncover a differential effect of Notch, whereby high Notch activity is associated with stem/progenitor cell expansion in the mouse embryo, yet it promotes reversible cell cycle exit in the foetus and the appearance of an adult muscle stem cell state. We propose that active Notch signalling is sufficient to sustain an upstream population of muscle founder stem cells while suppressing differentiation. Significantly, Notch does not override other signals that promote temporal myogenic cell fates during ontology where spatiotemporal developmental cues produce distinct phenotypic classes of myoblasts.
Solitary pulmonary adenofibroma in a middle-aged man with bladder cancer

Declaration of patient consent The authors certify that they have obtained all appropriate patient consent forms. In the form the patient(s) has/have given his/her/their consent for his/her/their images and other clinical information to be reported in the journal. The patients understand that their names and initials will not be published and due efforts will be made to conceal their identity, but anonymity cannot be guaranteed.
Carbon-doped Ge2Sb2Te5 phase-change memory devices featuring reduced RESET current and power consumption

In this paper, carbon-doped Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub>, integrating from 5% to 15% of carbon content, is studied as an alternative phase-change material. Accurate electrical characterizations were performed both on large and shrinked PCM devices. Compared to pure Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub> based reference devices, a wide decrease of about 50% of the RESET current, which translates into a RESET power reduction of about 25%, is observed when 5% of carbon is added to Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub>. Moreover, an improved endurance up to 10<sup>8</sup> cycles is obtained while maintaining a programming window higher than 2 orders of magnitude. An increase of about 30% of the activation energy for the crystallization process is also observed. Therefore, this paper suggests that Ge<sub>2</sub>Sb<sub>2</sub>Te<sub>5</sub> doped with 5% of carbon is a promising phase-change material for future PCM technology.
Scrubbing During Learning In Real-time Heuristic Search

Real-time agent-centered heuristic search is a well-studied problem where an agent that can only reason locally about the world must travel to a goal location using bounded computation and memory at each step. Many algorithms have been proposed for this problem and theoretical results have also been derived for the worst-case performance with simple examples demonstrating worst-case performance in practice. Lower bounds, however, have not been widely studied. In this paper we study best-case performance more generally and derive theoretical lower bounds for reaching the goal using LRTA*, a canonical example of a real-time agent-centered heuristic search algorithm. The results show that, given some reasonable restrictions on the state space and the heuristic function, the number of steps an LRTA*-like algorithm requires to reach the goal will grow asymptotically faster than the state space, resulting in "scrubbing" where the agent repeatedly visits the same state. We then show that while the asymptotic analysis does not hold for more complex realtime search algorithms, experimental results suggest that it is still descriptive of practical performance.
Hybrid Computational Model of High-Current Vacuum Arcs With External Axial Magnetic Field

This paper deals with the computer modeling of a high-current (total current ≥10 kA) vacuum arc with an external axial magnetic field. This arc is typical for certain kind of vacuum interrupters. The described hybrid model treats electrons as a massless fluid and ions as macroparticles. The macroparticle dynamics are calculated with the use of the particle-in-cell method. Ion-ion Coulomb collision is considered with the use of the Monte Carlo method. The model can simulate high-current vacuum arcs as a whole including separate cathode plasma jets, mixing zone, and common plasma column. The hybrid model is able to calculate V-shape volt-tesla characteristics, which correlate well with experimental results.
Dynamics of the Dorsal morphogen gradient

The dorsoventral (DV) patterning of the Drosophila embryo depends on the nuclear localization gradient of Dorsal (Dl), a protein related to the mammalian NF-κB transcription factors. Current understanding of how the Dl gradient works has been derived from studies of its transcriptional interpretation, but the gradient itself has not been quantified. In particular, it is not known whether the Dl gradient is stable or dynamic during the DV patterning of the embryo. To address this question, we developed a mathematical model of the Dl gradient and constrained its parameters by experimental data. Based on our computational analysis, we predict that the Dl gradient is dynamic and, to a first approximation, can be described as a concentration profile with increasing amplitude and constant shape. These time-dependent properties of the Dl gradient are different from those of the Bicoid and MAPK phosphorylation gradients, which pattern the anterior and terminal regions of the embryo. Specifically, the gradient of the nuclear levels of Bicoid is stable, whereas the pattern of MAPK phosphorylation changes in both shape and amplitude. We attribute these striking differences in the dynamics of maternal morphogen gradients to the differences in the initial conditions and chemistries of the anterior, DV, and terminal systems.
Region-Based PDEs for Cells Counting and Segmentation in 3D+Time Images of Vertebrate Early Embryogenesis

This paper is devoted to the segmentation of cell nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. The segmentation allows to identify and quantify the number of cells in the animal model. This kind of information is relevant to estimate important biological parameters such as the cell proliferation rate in time and space. Our approach is based on the active contour model without edges. We compare two different formulations of the model equation and evaluate their performances in segmenting nuclei of different shapes and sizes. Qualitative and quantitative comparisons are performed on both synthetic and real data, by means of suitable gold standard. The best approach is then applied on a number of time lapses for the segmentation and counting of cells during the development of a zebrafish embryo between the sphere and the shield stage.
A face detection method based on corner verifying

Face detection is the first step for automatic face recognition system and many surveillance systems, it has been widely applied in many fields. A face detection method based on corner verifying is presented. Firstly, most of the background area is quickly filtered out by skin color detection. Then faces are detected by AdaBoost face detection algorithm combination with skin color detection, but there are some non-faces to be detected. Finally, the faces are verified by corner distribution of human face after Harris corner detection to further reduce the error rate. Experimental results show that this method can efficiently and accurately detect the faces with multi-feature fusion.
Real-time unsupervised classification of web documents

This paper adresses the problem of clustering dynamic collections of web documents. We show an iterative algorithm based on a fine-grained keyword extraction (simple, compound words and proper nouns). Each new document inserted in the collection is either assigned to an existing class containing documents of the same topic, or assigned to a new class. After each step, when necessary, classes are refined using statistical techniques. The implementation of this algorithm was successfully integrated in an application used for Information Intelligence.
An Efficient Analysis for Reliable Data Transmission in Wireless Sensor Network

Ubiquitous technology through sensor networks is being applied to numerous industrial fields specially to increase the quality of human life (QoL). Therefore, Wireless Sensor Networks (WSNs) lossless data is one of the communications challenges to provide accurate data. Although, end-to-end data retransmission has evolved as a reliable transportation in Internet, this method is not applicable to WSNs due to the lack of reliability of wireless link and resource constraints in sensor nodes. In our previous paper, we proposed a reliable data transfer using path-reliability and implicit ACK called RTOD on WSN. However, path reliability calculation components such as RSSI, channel error rate, number of transmission in RTOD method have not been studied thoroughly. In this paper, we analysis path reliability components and simulate by using NS-2. Moreover, we propose limited number of transmission method (LTM) for WSNs. Proposed scheme shows average 4.1% fault tolerance.
Day-to-Day variation of the urine protein: creatinine ratio in female dogs with stable glomerular proteinuria caused by X-linked hereditary nephropathy.

BACKGROUND Interpretation of serial urine protein:creatinine (UPC) values is confounded by a lack of data regarding random biologic variation of UPC values in dogs with stable glomerular proteinuria. HYPOTHESIS That there is minimal day-to-day variability in the UPC of dogs with unchanging proteinuria and the number of measurements needed to reliably estimate UPC varies with the magnitude of proteinuria. ANIMALS Forty-eight heterozygous (carrier) female dogs with X-linked hereditary nephropathy (XLHN) causing stable proteinuria. METHODS Urine samples were obtained daily by cystocentesis for 3 consecutive days on 183 occasions (549 samples). The UPC was measured for each sample with a single dry-film chemistry auto-analyzer. Data were analyzed retrospectively by a power of the mean model because the variance of UPC values within the 3-day evaluation periods increased as the magnitude of proteinuria increased. RESULTS To demonstrate a significant difference (P < .05) between serial values in these proteinuric dogs, the UPC must change by at least 35% at high UPC values (near 12) and 80% at low UPC values (near 0.5). One measurement is adequate to reliably estimate the UPC when UPC <4, but 2-5 determinations are necessary at higher UPC values. CONCLUSIONS AND CLINICAL IMPORTANCE These guidelines for interpretation of serial UPC values in female dogs with XLHN may also be helpful for interpretation of UPC values in dogs with other glomerulopathies.
Pediatric Conjunctivitis and Air Pollution Exposure: A Prospective Observational Study

ABSTRACT Purpose: To investigate, in pediatric patients, the rate and clinical features of unspecific conjunctivitis of unknown origin (UCUO) and to evaluate their relationship with air pollution. Methods: From January to December 2013, we consecutively screened all of the patients referred for symptomatic ocular surface inflammation. Inclusion criteria for this study were age<14, diagnosis of conjunctivitis, residence in the Lombardia region. UCUO was defined as conjunctivitis of unknown etiology, not clearly due to infection or allergy. Based on addresses of residence and sites of 73 automatic air pollution monitoring stations (locations and mean annual particulate matter (PM) 10 and 2.5 concentrations were provided by the Regional Environmental Protection Agency (ARPA) Lombardia), each patient was paired with a value of exposure to PM. Relationship between UCUO and PM exposure was investigated. Results: A total of 132 of 251 screened children were included in this study. UCUO was diagnosed in 48/132 patients. The most common symptoms and signs in UCUO children were foreign body sensation (37/48) and conjunctival hyperemia (45/48), respectively. PM10 exposure value was significantly higher in UCUO (33.5±5.4µg/m3) compared to other groups (P<0.001, ANOVA). UCUO/total conjunctivitis ratio was significantly higher in residents in areas with more than 75 (Q3) days/year exceeding 50µg/m3 (EU legal limit) compared to areas with less than 45 (Q1) exceedances/year: 24/39: 61% vs 8/35: 23%; P>0.001, Chi-square test. Conclusion: Our data suggest a relationship between UCUO and air pollution. This form of conjunctivitis is not rare in pediatric patients and may be the most frequent in most polluted areas.
Sequence Analysis of the Cas1 Gene in Riemerella anatipestifer

Objective: The aim was to analyze Riemerella anatipestifer (RA) Cas1 gene and acquire more useful information for guiding the further study of the gene. Methods: Using bioinformatics method, sequence analysis of RA Cas1 gene was carried out with some databases and software. Results: Composition analysis of RA Cas1 gene, and homology search, sequence alignment, phylogenetic tree analysis and physicochemical property analysis of RA Cas1 protein were performed. Homology search revealed that Cas1 protein sequence of R. anatipestifer showed high similarity to those of strains within the Genus Capnocytophaga and Chryseobacterium, in accordance with the result of multiple sequence alignment and phylogenetic tree analysis. The rare codon analysis showed that there was little rare codon string in RA Cas1 gene. Conclusion: Cas1 gene of R. anatipestifer was evolutionally closely related to those of the Genus Capnocytophaga and Chryseobacterium, and can be over-expressed in E.coli without considering the impact of rare codons on translation.
Reduction of Peak Input Currents during Charge Pump Boosting in Monolithically Integrated High-Voltage Generators

This paper describes two methods for the reduction of the peak input current during the boosting of Dickson charge pumps. Both methods are implemented in the fully integrated Dickson charge pumps of a high-voltage display driver chip for smart-card applications. Experimental results reveal good correspondence with Spice simulations and show a reduction of the peak input current by a factor of 6 during boosting.
Combinatorial Mixtures of Multiparameter Distributions: An Application to Bivariate Data

Abstract: We introduce combinatorial mixtures – a flexible class of models for inference on mixture distributions whose components have multidimensional parameters. The key idea is to allow each element of the component-specific parameter vectors to be shared by a subset of other components. This approach allows for mixtures that range from very flexible to very parsimonious and unifies inference on component-specific parameters with inference on the number of components. We develop Bayesian inference and computational approaches for this class of distributions, and illustrate them in an application. This work was originally motivated by the analysis of cancer subtypes: in terms of biological measures of interest, subtypes may be characterized by differences in location, scale, correlations or any of the combinations. We illustrate our approach using publicly available data on molecular subtypes of lung and prostate cancers.
Herpes simplex virus glycoproteins gC-1 and gC-2 bind to the third component of complement and provide protection against complement- mediated neutralization of viral infectivity

Cells infected with herpes simplex virus type 1 (HSV-1) form rosettes with C3b-coated erythrocytes, whereas cells infected with herpes simplex virus type 2 (HSV-2) or other herpes viruses do not. It was reported that glycoprotein C of HSV-1 (gC-1) mediates the binding of C3b-coated erythrocytes to infected cells and has regulatory (decay- accelerating) activity for the alternative pathway C3 convertase of human complement. We show here that solubilized gC-1 binds to iC3- Sepharose affinity columns. We also report that solubilized gC-2, the genetically related glycoprotein specified by HSV-2, binds to iC3- Sepharose. mAb specific for gC-1 or gC-2 and mutant viral strains were used to identify the C3-binding glycoproteins. In other experiments, HSV-1 mutant strains and recombinants, differing only in their expression of gC, were tested for sensitivity to neutralization by human complement in the presence or absence of antibodies specific for HSV gD. In either case the gC- strain was most sensitive. Expression of gC-1 or gC-2 by isogenic insertion mutants provided protection against complement-mediated neutralization. These results indicate that the genetically and structurally related gC-1 and gC-2 share the functional activity of binding to human C3 and enhance viral infectivity.
An evaluation of AJAX-enabled java-based web application frameworks

When building rich user experience web applications, an abundance of web application frameworks is available and only little guidance for making the decision which one to choose. The objective of this study was to evaluate AJAX-enabled, Java-based web application frameworks for adaptation in our project and to devise an economical method to conduct such evaluations. The method we propose mixes comparative analysis and scenario-based empirical evaluation for selection of best-suited web application framework from limited number of candidates. This multi-method approach proved to demonstrate differences in the frameworks that were not practically observable using elemental method. The results suggest that the method we propose would also be applicable for other projects.
A little advice can be very helpful

Proving superpolylogarithmic lower bounds for dynamic data structures has remained an open problem despite years of research. Recently, Patrascu proposed an exciting new approach for breaking this barrier via a two player communication model in which one player gets private advice at the beginning of the protocol. He gave reductions from the problem of solving an asymmetric version of set-disjointness in his model to a diverse collection of natural dynamic data structure problems in the cell probe model. He also conjectured that, for any hard problem in the standard two-party communication model, the asymmetric version of the problem is hard in his model, provided not too much advice is given. In this paper, we prove several surprising results about his model. We show that there exist Boolean functions requiring linear randomized communication complexity in the two-party model, for which the asymmetric versions in his model have deterministic protocols with exponentially smaller complexity. For set-disjointness, which also requires linear randomized communication complexity in the two-party model, we give a deterministic protocol for the asymmetric version in his model with a quadratic improvement in complexity. These results demonstrate that Patrascu's conjecture, as stated, is false. In addition, we show that the randomized and deterministic communication complexities of problems in his model differ by no more than a logarithmic multiplicative factor. We also prove lower bounds in some restricted versions of this model for natural functions such as set-disjointness and inner product. All of our upper bounds conform to these restrictions.