Miracle-dz/UniFAR-FTUs huggingface dataset:
Selective Histocompatibility Leukocyte Antigen (Hla)-A2 Loss Caused by Aberrant Pre-mRNA Splicing in 624mel28 Melanoma Cells

Histocompatibility leukocyte antigen (HLA)-A2 is used as a restricting element to present several melanoma-associated antigen (MAA)-derived peptides to cytotoxic T lymphocytes (CTLs). HLA-A2 antigen is selectively lost in primary melanoma lesions and more frequently in metastases. Only scanty information is available about the molecular mechanisms underlying this abnormality, in spite of its potentially negative impact on the clinical course of the disease and on the outcome of T cell–based immunotherapy. Therefore, in this study we have shown that the selective HLA-A2 antigen loss in melanoma cells 624MEL28 is caused by a splicing defect of HLA-A2 pre-mRNA because of a base substitution at the 5′ splice donor site of intron 2 of the HLA-A2 gene. As a result, HLA-A2 transcripts are spliced to two aberrant forms, one with exon 2 skipping and the other with intron 2 retention. The latter is not translated because of an early premature stop codon in the retained intron. In contrast, the transcript with exon 2 skipping is translated to a truncated HLA-A2 heavy chain without the α1 domain. Such a polypeptide is synthesized in vitro but is not detectable in cells, probably because of the low steady state level of the corresponding mRNA and the low translation efficiency. These results indicate that a single mutational event in an HLA class I gene is sufficient for loss of the corresponding allele. This may account, at least in part, for the high frequency of selective HLA class I allele loss in melanoma cells. Our conclusion emphasizes the need to implement active specific immunotherapy with a combination of peptides presented by various HLA class I alleles. This strategy may counteract the ability of melanoma cells with selective HLA class I allele loss to escape from immune recognition.
Development of a Swarm UAV Simulator Integrating Realistic Motion Control Models For Disaster Operations

Simulation environments for Unmanned Aerial Vehicles (UAVs) can be very useful for prototyping user interfaces and training personnel that will operate UAVs in the real world. The realistic operation of such simulations will only enhance the value of such training. In this paper, we present the integration of a model-based waypoint navigation controller into the Reno Rescue Simulator for the purposes of providing a more realistic user interface in simulated environments. We also present potential uses for such simulations, even for real-world operation of UAVs.
The intravesical ureter in children with vesicoureteral reflux: a morphological and immunohistochemical characterization.

PURPOSE We investigated intravesical ureteral endings using immunohistochemical methods to study general morphology, smooth muscle architecture and collagen composition in children with vesicoureteral reflux. MATERIALS AND METHODS Samples were obtained from 29 ureterorenal units in children with a mean age of 52.3 months undergoing reflux surgery. Routine histological paraffin embedded sections were stained with hematoxylin and eosin, and Masson trichrome to assess general morphology. Staining for actin, myosin and desmin was performed to evaluate the presence, allocation and architecture of the ureteral smooth muscle wrap. In addition, indirect immunohistochemical methods were used to study the collagen composition of the ureteral wall and CD68 was used for macrophage labeling as a marker of tissue remnant scavenging. All investigations were done using high power field magnification for quantification. In addition, age matched, nonrefluxing ureteral specimens served as controls. RESULTS Smooth muscle alpha-actin, myosin and desmin expression were extensively decreased in all specimens pertaining to the ureteral ending. This distal part showed a high degree of muscle atrophy and degeneration as well as a disordered fiber arrangement associated with increased extracellular matrix collagen accumulation. In addition, CD68 positive macrophages were significantly increased. In contrast to these observations, the proximal intravesical portion of the ureter showed intact morphology and arrangement of the muscular coat. CONCLUSIONS Refluxing intravesical ureteral endings showed dysplasia, atrophy and architectural derangement of smooth muscle fibers. Consequently symmetrical contraction of the distal ureteral smooth muscle coat creating the active valve mechanism to protect reflux is not achievable.
Consumer Surplus in the Digital Economy: Estimating the Value of Increased Product Variety at Online Booksellers

We present a framework and empirical estimates that quantify the economic impact of increased product variety made available through electronic markets. While efficiency gains from increased competition significantly enhance consumer surplus, for instance, by leading to lower average selling prices, our present research shows that increased product variety made available through electronic markets can be a significantly larger source of consumer surplus gains.One reason for increased product variety on the Internet is the ability of online retailers to catalog, recommend, and provide a large number of products for sale. For example, the number of book titles available at Amazon.com is more than 23 times larger than the number of books on the shelves of a typical Barnes & Noble superstore, and 57 times greater than the number of books stocked in a typical large independent bookstore.Our analysis indicates that the increased product variety of online bookstores enhanced consumer welfare by $731 million to $1.03 billion in the year 2000, which is between 7 and 10 times as large as the consumer welfare gain from increased competition and lower prices in this market. There may also be large welfare gains in other SKU-intensive consumer goods such as music, movies, consumer electronics, and computer software and hardware.
Extracting Topological Information from Grid Maps for Robot Navigation

In many robotic navigation-related tasks, abstracting the environment where mobile robots carry out some mission can be of a great benefit. In particular, extracting a simple topological graph-like representation from a more complex and detailed metric map is often required for path-planning and navigation. In this work, an approach to perform such extraction in grid maps is presented. The focus is not only on obtaining a diagram or visual representation of possible paths, but also to propose a new way to obtain graph data information related to the connectivity of the environment that can be passed to robots or to a centralized planner, in order to assist the navigation task. The approach proposed is based on image processing techniques. Simulation results prove its simplicity, accuracy and efficiency.
First Results From the Phenology-Based Synthesis Classifier Using Landsat 8 Imagery

A fully automatic phenology-based synthesis (PBS) classification algorithm was developed to map land cover based on medium spatial resolution satellite data using the Google Earth Engine cloud computing platform. Vegetation seasonality, particularly in the tropical dry regions, can lead conventional algorithms based on a single date image classification to “misclassify” land cover types, as the selected date might reflect only a particular stage of the natural phenological cycle. The PBS classifier operates with occurrence rules applied to a selection of single date image classifications of the study area to assign the most appropriate land cover class. Since the launch of Landsat 8 in 2013, it has been possible to acquire imagery at any point on the Earth every 16 days with exceptional radiometric quality. The relatively high global acquisition frequency and the open data policy allow near-real-time land cover mapping and monitoring with automated tools such as the PBS classifier. We mapped four protected areas and their 20-km buffer zones from different ecoregions in Sub-Saharan Africa using the PBS classifier to present its first results. Accuracy assessment was carried out through a visual interpretation of very high resolution images using a Web geographic information system interface. The combined overall accuracy was over 90%, which demonstrates the potential of the classifier and the power of cloud computing in geospatial sciences.
Chapter 1 Moving Cast Shadows Detection Methods for Video Surveillance Applications

Moving cast shadows are a major concern in today’s performance from broad range of many vision-based surveillance applications because they highly difficult the object classification task. Several shadow detection methods have been reported in the literature during the last years. They are mainly divided into two domains. One usually works with static images, whereas the second one uses image sequences, namely video content. In spite of the fact that both cases can be analogously analyzed, there is a difference in the application field. The first case, shadow detection methods can be exploited in order to obtain additional geometric and semantic cues about shape and position of its casting object (’shape from shadows’) as well as the localization of the light source. While in the second one, the main purpose is usually change detection, scene matching or surveillance (usually in a background subtraction context). Shadows can in fact modify in a negative way the shape and color of the target object and therefore affect the performance of scene analysis and interpretation in many applications. This chapter wills mainly reviews shadow detection methods as well as their taxonomies related with the second case, thus aiming at those shadows which are associated with moving objects (moving shadows). Ariel Amato Computer Vision Center, Universitat Autònoma de Barcelona, e-mail: aamato@cvc.uab. es Ivan Huerta Institut de Robòtica i Informàtica industrial, Universitat Politècnica de Catalunya, e-mail:
Systematic review of atomoxetine data in childhood and adolescent attention-deficit hyperactivity disorder 2009–2011: Focus on clinical efficacy and safety

Background: Clinicians obtain critical prescribing knowledge from clinical papers and review articles. This is the first published systematic review of clinical atomoxetine data covering 2009–2011. Objective: We aim to update clinicians on current clinical atomoxetine data with specific reference to time of onset of efficacy and maximal efficacy. These data may allow critical analysis of comparative efficacy between atomoxetine and stimulant medications. Methods: A formal systematic review of atomoxetine data from January 2009–June 2011 was conducted. The search term used was “atomoxetine” in the English language. The search yielded 747 citations from which 106 are clinical data. This paper includes clinical efficacy and safety data and excludes quality-of-life and review papers. Results: Atomoxetine has an onset of action within 4 weeks (possibly within 1 week in subsequent responders) but requires at least 12 weeks for full response to be demonstrated. Treatment-naïve cohorts (6–12 weeks) report effect sizes of 0.6–1.3. Using minimum 6-week clinical trial criteria, atomoxetine may demonstrate similar efficacy to methylphenidate comparing reduction in core ADHD symptoms in meta-analysis, although the diversity of the data makes interpretation complex. From epidemiological databases, cardiovascular and suicide-related events were similar to those seen in patients taking methylphenidate. Conclusions: Incremental response time to atomoxetine should be considered in the design of future comparative efficacy trials.
Congestion-driven codesign of power and signal networks

Presents a global wire design methodology that simultaneously considers the performance needs for both signal lines and power grids under congestion considerations. An iterative procedure is employed in which the global routing is performed according to a congestion map that includes the resource utilization of the power grid, followed by a step in which the power grid is adjusted to relax the congestion in crowded regions. This adjustment is in the form of wire removal in noncritical regions, followed by a wire sizing step that overcomes the effects of wire removal. Experimental results show that the overall routability can be significantly improved while the power grid noise is maintained within the voltage droop constraint.
SDF2L1 interacts with the ER-associated degradation machinery and retards the degradation of mutant proinsulin in pancreatic &bgr;-cells

Summary Stromal cell-derived factor 2-like 1 (SDF2L1) is an endoplasmic reticulum (ER)-localized protein whose function is undefined. Here we show that SDF2L1 protein levels are increased in response to ER stress-inducing compounds, but not other cell stressors that we tested in insulinoma cell lines. SDF2L1 protein levels were also induced by expression of misfolded proinsulin in insulinoma cells and in islets from diabetic mice. Immunoprecipitation and binding assays demonstrated that SDF2L1 interacts with the ER chaperone GRP78/BiP, the ER-associated degradation (ERAD) machinery and with misfolded proinsulin. Unexpectedly, knockdown of SDF2L1 in INS-1 (insulin 2 C96Y-GFP) cells increased the degradation kinetics of mutant proinsulin, suggesting that SDF2L1 regulates substrate availability for the ERAD system. We suggest that SDF2L1 increases the time that misfolded proteins have to achieve a correctly folded conformation and thus that SDF2L1 can act as a buffer for substrate availability for ERAD in pancreatic &bgr;-cells.
Induction and Recapitulation of Deep Musical Structure

We describe recent extensions to our framework for the automatic generation of music-making programs. We have previously used genetic programming techniques to produce musicmaking programs that satisfy user-provided critical criteria. In this paper we describe new work on the use of connectionist techniques to automatically induce musical structure from a corpus. We show how the resulting neural networks can be used as critics that drive our genetic programming system. We argue that this framework can potentially support the induction and recapitulation of deep structural features of music. We present some initial results produced using neural and hybrid symbolic/neural critics, and we discuss directions for future work.
Significance-aware Hammerstein group models for nonlinear acoustic echo cancellation

In this work, a novel approach for nonlinear acoustic echo cancellation is proposed. The main innovative idea of the proposed method is to model only the small region of the echo path around the direct path by a group of parallel Hammerstein models, to estimate a nonlinear preprocessor by correlations between the linear kernels of the Hammerstein submodels, and to describe the remaining echo path by a simple Hammerstein model with the preprocessor determined in the aforementioned way. While the computational complexity of such a system increases only slightly in comparison to a linear echo canceller, experiments with speech recordings from a smartphone in different environments confirm a significantly increased echo cancellation performance.
Finite Sample Error Bound for Parzen Windows

Parzen Windows as a nonparametric method has been applied to a variety of density estimation as well as classification problems. Similar to nearest neighbor methods. Parzen Windows does not involve learning. While it converges to true but unknown probability densities in the asymptotic limit, there is a lack of theoretical analysis on its performance with finite samples. In this paper we establish a finite sample error bound for Parzen Windows. We first show that Parzen Windows is an approximation to regularized least squares (RLS) methods that have been well studied in statistical learning theory. We then derive the finite sample error bound for Parzen Windows, and discuss the properties of the error bound and its relationship to the error bound for RLS. This analysis provides interesting insight to Parzen Windows as well as the nearest neighbor method from the point of view of learning theory. Finally, we provide empirical results on the performance of Parzen Windows and other methods such as nearest neighbors, RLS and SVMs on a number of real data sets. These results corroborate well our theoretical analysis.
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes

The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network. NCG also stores information on all primary interactors of cancer proteins, thus providing a complete overview of 5357 proteins that constitute direct and indirect determinants of human cancer. With the constant delivery of results from the mutational screenings of cancer genomes, NCG represents a versatile resource for retrieving detailed information on particular cancer genes, as well as for identifying common properties of precompiled lists of cancer genes. NCG is freely available at: http://bio.ifom-ieo-campus.it/ncg.
Decentralized control for multimachine power system: A new approach

In this paper, a decentralized control problem is considered for multimachine power system. First, a novel mathematical model of multimachine power systems is developed. The main characteristic of this model is that interactions between generators and changes in operating conditions are represented by time-varying parameters. Second, it develops a decentralized controller for the transient stabilization and voltage regulation. The methodology adopted is based on backstepping design strategy. Case studies are achieved in a two-area four machine power system to verify the effectiveness of the approach. Simulation results show that the proposed approach gain much priority over traditional AVR/PSS in damping power oscillation, and improving voltage regulation.
Sketch abstractions for character posing

We propose a sketch-based posing system for rigged 3D characters that allows artists to create custom sketch abstractions on top of a character's actual shape. A sketch abstraction is composed of rigged curves that form an iconographic 2D representation of the character from a particular viewpoint. When provided with a new input sketch, our optimization system minimizes a nonlinear iterative closest point energy to find the rigging parameters that best align the character's sketch abstraction to the input sketch. A custom regularization term addresses the underconstrained nature of the problem to select favorable poses. Although our system supports arbitrary black-box rigs, we show how to optimize computations when rigging formulas and derivatives are available. We demonstrate our system's flexibility with examples showing different artist-designed sketch abstractions for both full body posing and the customization of individual components of a modular character. Finally, we show that simple sketch abstractions can be built on the fly by projecting a drawn curve onto the character's mesh. Redrawing the curve allows the user to dynamically pose the character. Taken together, our system enables a new form of intuitive sketch-based posing in which the character designer has the freedom to prescribe the sketch abstraction that is most meaningful for the character.
Insect midgut carboxypeptidases with emphasis on S10 hemipteran and M14 lepidopteran carboxypeptidases

We compared the whole complement of midgut carboxypeptidases from 10 insects pertaining to five orders based on transcriptomes obtained by deep sequencing and biochemical data. Most of the carboxypeptidases were metallocarboxypeptidases from family M14, with carboxypeptidase A (CPA) predominating over carboxypeptidase B (CPB). They were found in all of the insects studied except for the hemipterans and a bruchid beetle. M14 carboxypeptidases were expressed only in the midgut of Spodoptera frugiperda (Lepidoptera). The most expressed CPA from this insect (SfCPA) was cloned, sequenced and expressed as a recombinant enzyme. This enzyme was used to generate antibodies used to demonstrate that SfCPA is secreted by an exocytic route. Serine carboxypeptidases from family S10 were found in all of the insects studied here. In S. frugiperda, they are expressed in all tissues besides the midgut, in accordance with their presumed lysosomal role. In the hemipteran Dysdercus peruvianus, S10 carboxypeptidases are expressed only in midgut, suggesting that they are digestive enzymes. This was confirmed by enzyme assays of midgut contents. Furthermore, the substrate specificity of D. peruvianus S10 carboxypeptidases are predicted to be one CPC (preferring hydrophobic residues) and one CPD (preferring basic residues), thus able to hydrolyse the peptides formed by their digestive cathepsin D and cathepsin L, respectively. The role of S10 carboxypeptidases in bruchid beetles are suggested to be the same as in hemipterans.
Measurement of Radial Peripapillary Capillary Density in the Normal Human Retina Using Optical Coherence Tomography Angiography

Aim: To image the radial peripapillary capillary (RPC) network with optical coherence tomography angiography (OCTA) and measure its capillary density (CD) in the normal human retina. Materials and Methods: Fifty-two normal participants underwent OCTA imaging with RTVue XR 100 Avanti OCT. The angioflow enface RPCs network was extracted from OCTA and 8 peripapillary sectors with a sector angle of 45 degrees were selected for quantitative analysis: superior nasal, superior temporal, temporal upper, temporal lower, nasal upper, nasal lower, inferior nasal, and inferior temporal. CD was measured within a 3.4-mm circle diameter around the optic nerve head (ONH) using the Bar-Selective Combination of Shifted Filter Responses method. Results: Using OCTA, the RPC network was visualized with excellent detail as a distinctive pattern of parallel, long, uniform-diameter vessels around ONH, oriented parallel to the retinal nerve fiber layer. The mean overall RPC density within the circle diameter of 3.4 mm around ONH was 0.21±0.053 (95% confidence interval: 0.204-0.216). The CD at the superior temporal (0.243±0.045) and inferior temporal (0.242±0.047) sectors was higher (P<0.05) when compared with the other sectors. Age, sex (P=0.7), and disc size (P=0.3) did not have a significant effect on CD measurement. Conclusions: We imaged and describe a reproducible method to measure the RPC density, which would help us to understand the role of this vascular bed in the functioning of the retinal nerve fiber layer. Our study demonstrated that there was symmetry in superior and inferior corresponding pair sectors with respect to the horizontal meridian and symmetry between paired sectors at the nasal and temporal poles with respect to the vertical meridian.