Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic verification of Java design patterns

Design patterns are widely used by object oriented designers and developers for building complex systems in object oriented programming languages such as Java. However, systems evolve over time, increasing the chance that the pattern in its original form will be broken. We attempt to show that many design patterns (implemented in Java) can be verified automatically. Patterns are defined in terms of variants, mini-patterns, and artifacts in a pattern description language called SPINE. These specifications are then processed by Hedgehog, an automated proof tool that attempts to prove that Java source code meets these specifications.
Weighted Sampling From Landmark Windows Over Data Streams

There are growing interests in algorithms for processing and querying continuous data streams recently. This paper introduces the problem of sampling from landmark windows over data streams and presents a weighted stratified multistage sampling (WSMS) algorithm for this problem. The algorithm extends the classic reservoir-sampling algorithm and the weighted sampling algorithm with a reservoir by using basic window technique, and works well even when the number of data items in the landmark window varies dramatically over time. The theoretic analysis and experiments show that the algorithm is effective and efficient for continuous data streams processing
Ventricular Bigeminy after Subcutaneous Administration of Apomorphine in a Patient with Refractory Parkinson’s Disease: A Case Report

Apomorphine is a well established treatment for the management of sudden, unexpected and refractory levodopa-induced “off” states in fluctuating Parkinson’s disease either as bolus injections or as continuous infusions. Incidents of atrial fibrillation associated with the administration of the drug have been reported in the past but no incidents of ventricular arrhythmias. We report a case of ventricular bigeminy recorded in a female patient after the administration of apomorphine.
Hox gene regulation in the central nervous system of Drosophila

Hox genes specify the structures that form along the anteroposterior (AP) axis of bilateria. Within the genome, they often form clusters where, remarkably enough, their position within the clusters reflects the relative positions of the structures they specify along the AP axis. This correspondence between genomic organization and gene expression pattern has been conserved through evolution and provides a unique opportunity to study how chromosomal context affects gene regulation. In Drosophila, a general rule, often called “posterior dominance,” states that Hox genes specifying more posterior structures repress the expression of more anterior Hox genes. This rule explains the apparent spatial complementarity of Hox gene expression patterns in Drosophila. Here we review a noticeable exception to this rule where the more-posteriorly expressed Abd-B Hox gene fails to repress the more-anterior abd-A gene in cells of the central nervous system (CNS). While Abd-B is required to repress ectopic expression of abd-A in the posterior epidermis, abd-A repression in the posterior CNS is accomplished by a different mechanism that involves a large 92 kb long non-coding RNA (lncRNA) encoded by the intergenic region separating abd-A and Abd-B (the iab8ncRNA). Dissection of this lncRNA revealed that abd-A is repressed by the lncRNA using two redundant mechanisms. The first mechanism is mediated by a microRNA (mir-iab-8) encoded by intronic sequence within the large iab8-ncRNA. Meanwhile, the second mechanism seems to involve transcriptional interference by the long iab-8 ncRNA on the abd-A promoter. Recent work demonstrating CNS-specific regulation of genes by ncRNAs in Drosophila, seem to highlight a potential role for the iab-8-ncRNA in the evolution of the Drosophila Hox complexes.
Hyaluronan, a Crucial Regulator of Inflammation

Hyaluronan (HA), a major component of the extracellular matrix (ECM), plays a key role in regulating inflammation. Inflammation is associated with accumulation and turnover of HA polymers by multiple cell types. Increasingly through the years, HA has become recognized as an active participant in inflammatory, angiogenic, fibrotic, and cancer promoting processes. HA and its binding proteins regulate the expression of inflammatory genes, the recruitment of inflammatory cells, the release of inflammatory cytokines, and can attenuate the course of inflammation, providing protection against tissue damage. A growing body of evidence suggests the cell responses are HA molecular weight dependent. HA fragments generated by multiple mechanisms throughout the course of inflammatory pathologies, elicit cellular responses distinct from intact HA. This review focuses on the role of HA in the promotion and resolution of inflammation.
Partial automation of an integrated reverse engineering environment of binary code

The constant development of newer and faster machines requires software to be made available on those new machines at a rate faster than what it takes to develop the software. The use of binary translation techniques to migrate software from one machine to another is effective-it makes software available in little time without incurring reprogramming costs. However the development of such a tool is in itself an issue, as with each new architecture, a new tool needs to be written. The author presents a partially automated integrated environment for the reverse engineering of binary or executable code. This environment is suitable for the development of disassemblers, binary translators and decompilers.
Perspective models as a means for achieving true representational accuracy

Accurate and expressive representation of the subject matter over which a context-oriented, decision-support system operates is fundamental to the effectiveness and longevity of the resulting solution. Often taking the form of an ontology, such extensive representational models, by their very nature, are rich in both relationships and fine-grained objects. It is, however, these two strengths that can significantly increase complexity for its users in addition to adversely affecting system performance. Further, due to the multitude of compartmentalized facets (i.e., populations of distinct, reasoning agents) inherent in such software solutions, it is important to recognize that a single-minded omniscient set of domain descriptions representing a singular view of the world is not necessarily appropriate for every ontology user. In fact, in such highly expressive environments, it is critical to not only accept these distinctions in user perspective, but to, in fact, promote and exploit them. It is by acknowledging and supporting this perspective-based individuality that true representational accuracy and utility is achieved. To be effective, the concept of perspective models must be partnered with a supportive model development process. In addition to an explanation of the concept of perspective models, this paper provides a discussion of a development process that supports effective development of both the potentially numerous set of perspective models in addition to the integration model that inter-connects them. The process offered in this paper effectively parcels the development of individual perspective models with the individuals possessing the necessary domain and use-case expertise. In this manner, the development process strives to significantly increase the involvement of the entire set of team members in the modeling activity, both capitalizing on user domain expertise in addition to increasing critical user understanding and acceptance of the representation over which their components are to operate
A Novel Scheme for the Fovea Localization on Retinal Images

Fovea is at the center of the macula, hard to be observed, but the mainly occurring region of diabetic retinopathy. Parabola-like vascular geometry model is the most common way used to detect fovea. Most studies took the center of an optic disc (OD) as the vertex of the parabola-like vasculature. According to the anatomic observation, the ideal vertex is the entry point of the main blood vessels (i.e. vessel origin (VO)), which is usually beside the OD center. Moreover, VO does not coincide with the OD center. Hence, a VO-parabolic fovea localization scheme, with VO as the vertex of the parabola-like vasculature, is proposed to get better fovea localization. In order to exactly extract vessel origins from retinal images, four features based on the characteristic of vessel origin are selected. Once the vessel origin in a retinal image is identified, the SR-Hough transform employs the vessel origin as the vertex to obtain the fittest parabola. Finally, the VO-parabolic scheme uses the symmetry axis of the fittest parabola to locate the fovea. Two public available databases, DRIVE and STARE, are employed to evaluate the proposed scheme. The experimental results show that the average Euclidean distance between the located position of fovea and the one marked by experts are respectively 9.8 pixels and 30.7 pixels in these two databases.
Channel viability of intra-vehicle optical wireless communications

This paper provides a first-of-its-kind look at the viability of the optical wireless channel for use in intra-vehicular communications applications. The analysis, focusing on the received power and bandwidth availability of an optical wireless system utilising a centrally located single infra-red LED within a sports utility vehicle, shows that the vehicle's passengers can take advantage of received powers up to 49 μW with bandwidths ≥ 300 MHz. Furthermore, interior regions such as the dashboard area are illuminated with a sufficient power and bandwidth that simple user-vehicle interfaces such as a window, air-conditioning or audio-visual controllers are highly plausible. The advantages of utilising optical wireless communications within the vehicle, is not only about increased bandwidth availability whilst maintaining allowable user mobility, but also the potential mitigation of radio frequency interference, lower system costs through the utilisation of license free spectrum and increasing manufacturing efficiency by lowering the complexity of copper cabling.
Pre-classification of points and segmentation of urban objects by scan line analysis of airborne

Currently available laser scanners are capable of performing hundreds of thousands of range measurements per second at a range resolution of a few centimeters. Despite that increasing performance, up to now airborne LiDAR mapping has established itself only in fields of application that do not require on-line data processing. A typical example in this context is urban modeling. We want to point out some other tasks like object recognition, situation analysis and on-line change detection that have come into reach of today's LiDAR technology. Primary goal of the work presented in this paper is the on-line data preparation for subsequent analysis. We present a workflow of real-time capable filter operations to detect the ground level and distinguish between clutter and manmade objects in airborne laser scanner data of urban regions. Based on interpretation of single scan lines, straight line segments are first segmented and then connected, and the resulting surfaces are delineated by a polygon. A preliminary step is done towards fast reconstruction of buildings for rapid city-modeling, co-registration or recognition of urban structures.
2016 Ieee International Conference on Big Data (big Data) Random Surfing on Multipartite Graphs

—Equipping an imaginary Random Surfer of the Web with the ability to teleport, was Page et al.'s creative way to justify a mathematical necessity; the Teleportation Matrix. Despite being essential for ensuring the ergodicity of the underlying Markov chain, the standard definition of this matrix treats the nodes of the graph in a simplistic and " leveling " way that can prove counterintuitive – especially for applications of the method on graphs of heterogeneous data. In this work, we focus on such graphs and we propose a novel alternative teleportation model that yields a well-defined ranking vector, while being as easy to handle as the traditional teleportation. We explore the theoretical implications of our model, and we reveal a wealth of nice properties that result to direct computational advantages over PageRank. We conduct a set of experiments using real-world datasets and we verify both the useful computational characteristics of our model and its favorable qualitative performance. Our promising findings suggest there remain more to be explored, and maybe much to be gained, by revisiting the teleportation model; a neglected part of PageRank that is typically taken for granted by the majority of applications in the literature.
Genetic Polymorphisms of Interleukin-1 Alpha and the Vitamin D Receptor in Mexican Mestizo Patients with Intervertebral Disc Degeneration

Intervertebral disc degeneration (IDD) is the most common diagnosis in patients with back pain, a leading cause of musculoskeletal disability worldwide. Several conditions, such as occupational activities, gender, age, and obesity, have been associated with IDD. However, the development of this disease has strong genetic determinants. In this study, we explore the possible association between rs1800587 (c.-949C>T) of interleukin-1 alpha (IL1A) and rs2228570 (c.2T>V) and rs731236 (c.1056T>C) of vitamin D receptor (VDR) gene polymorphisms and the development of IDD in northwestern Mexican Mestizo population. Gene polymorphisms were analyzed by polymerase chain reaction followed by restriction fragment length polymorphism, in two groups matched by age and gender: patients with symptomatic lumbar IDD (n = 100) and subjects with normal lumbar-spine MRI-scans (n = 100). Distribution of the mutated alleles in patients and controls was 27.0% versus 28.0% (P = 0.455) for T of rs1800587 (IL1A); 53.0% versus 58.0% (P = 0.183) for V of rs2228570 (VDR); and 18.0% versus 21.0% (P = 0.262) for C of rs731236 (VDR). Our results showed no association between the studied polymorphisms and IDD in this population. This is the first report on the contribution of gene polymorphisms on IDD in a Mexican population.
The Complete Chloroplast Genome Sequences of Three Veroniceae Species (Plantaginaceae): Comparative Analysis and Highly Divergent Regions

Previous studies of Veronica and related genera were weakly supported by molecular and paraphyletic taxa. Here, we report the complete chloroplast genome sequence of Veronica nakaiana and the related species Veronica persica and Veronicastrum sibiricum. The chloroplast genome length of V. nakaiana, V. persica, and V. sibiricum ranged from 150,198 bp to 152,930 bp. A total of 112 genes comprising 79 protein coding genes, 29 tRNA genes, and 4 rRNA genes were observed in three chloroplast genomes. The total number of SSRs was 48, 51, and 53 in V. nakaiana, V. persica, and V. sibiricum, respectively. Two SSRs (10 bp of AT and 12 bp of AATA) were observed in the same regions (rpoC2 and ndhD) in three chloroplast genomes. A comparison of coding genes and non-coding regions between V. nakaiana and V. persica revealed divergent sites, with the greatest variation occurring petD-rpoA region. The complete chloroplast genome sequence information regarding the three Veroniceae will be helpful for elucidating Veroniceae phylogenetic relationships.
Pure-Jump Lévy Processes and Self-decomposability in Financial Modeling

In this study, we review the connections between Lévy processes with jumps and self-decomposable laws. Self-decomposable laws constitute a subclass of infinitely divisible laws. Lévy processes additive processes and independent increments can be related using self-similarity property. Sato (1991) defined additive processes as a generalization of Lévy processes. In this way, additive processes are those processes with inhomogeneous (in general) and independent increments and Lévy processes correspond with the particular case in which the increments are time homogeneous. Hence Lévy processes are considerable as a particular type. Self-decomposable distributions occur as limit law an Ornstein-Uhlenbeck type process associated with a background driving Lévy process. Finally as an application, asset returns are representing by a normal inverse Gaussian process. Then to test applicability of this representation, we use the nonparametric threshold estimator of the quadratic variation, proposed by Cont and Mancini (2007).
Integration of Sensory Force Feedback Is Disturbed in CRPS-Related Dystonia

Complex regional pain syndrome (CRPS) is characterized by pain and disturbed blood flow, temperature regulation and motor control. Approximately 25% of cases develop fixed dystonia. The origin of this movement disorder is poorly understood, although recent insights suggest involvement of disturbed force feedback. Assessment of sensorimotor integration may provide insight into the pathophysiology of fixed dystonia. Sensory weighting is the process of integrating and weighting sensory feedback channels in the central nervous system to improve the state estimate. It was hypothesized that patients with CRPS-related dystonia bias sensory weighting of force and position toward position due to the unreliability of force feedback. The current study provides experimental evidence for dysfunctional sensory integration in fixed dystonia, showing that CRPS-patients with fixed dystonia weight force and position feedback differently than controls do. The study shows reduced force feedback weights in CRPS-patients with fixed dystonia, making it the first to demonstrate disturbed integration of force feedback in fixed dystonia, an important step towards understanding the pathophysiology of fixed dystonia.
Principe démocratique et décision en coopérative

A partir d’entretiens semi-directifs realises aupres des presidents de dix-huit cooperatives vinicoles de Gironde, auxquels il a ete demande de decrire et de juger le processus de decision en vigueur dans leur cooperative, cet article montre que le taux de participation des administrateurs (assimile au fonctionnement democratique de la cooperative) et l’existence d’un directeur salarie constituent les deux principaux facteurs determinant l’organisation du processus de decision des cooperatives. En depit de statuts identiques, les cooperatives usent du principe democratique de maniere tres inegale. Si les administrateurs, conformement aux statuts de la cooperation, prennent l’essentiel des decisions strategiques (76 %), leur contribution a l’ensemble du processus de decision est nettement plus discrete et limitee a quelques membres du bureau. Cependant, une participation plus intense n’a que peu de repercussions sur les modalites de la prise de decision (delais, opposition, votes negatifs, circulation de l’information).
Microtubule dynamics followed through cell differentiation and tissue biogenesis in C. elegans

Microtubules (MTs) are cytoskeletal filaments essential for many processes in eukaryotic cells. Assembled of tubulin subunits, MTs are dynamic structures that undergo successive and stochastic phases of polymerization and depolymerization, a behavior called dynamic instability. Dynamic instability has been extensively studied in cultured cells and in vitro using cytoplasmic extracts or reconstituted MTs. However, how MTs behave in intact tissues and how their dynamics are affected by or affect tissue function are poorly understood. Recent advances in high-resolution live imaging have helped overcome technical limitation in order to visualize MTs in intact living organisms including Drosophila or Caenorhabditis elegans. We recently took advantage of the well-characterized development, small size and transparency of C. elegans to monitor MT dynamics throughout tissue biogenesis with high spatial and temporal resolution. Using the sex myoblast lineage that generates the egg-laying muscles from 2 mitotic precursors, we identified selective dynamics in precursor versus differentiated cells, and molecular regulation of MT dynamics changes that occur during cell differentiation. We discuss here how this approach led to novel insights into the regulation of MTs dynamics and organization in vivo.
Making Events Less Slippery with eel

Event-driven programming divides a program's logical control flow into a series of callback functions, making its behavior difficult to follow. However, current program analysis techniques can preserve the event model while making event-driven code easier to read, write, debug and maintain. We designed the Explicit Event Library (libeel) to be amenable to program analysis, and created tools to graphically expose control flow, verify resource safety properties, and simplify debugging. The result sustains the advantages of event-driven programming while adding the important advantage of programmability.
Implementing in vivo cellular automata using toggle switch and inter-bacteria communication mechanism

Artificial genetic circuits have been recently proposed to realize unprecedented biological systems which do not exist in nature by combining several genes. For example, recombinant Escherichia coli provides novel artificial functions such as blinking periodically or invading cancer cells. In protein engineering, new functional proteins have been created by site-directed mutagenesis methods. The main purpose of our research is to implement the Cellular Automata (CA) in vivo employing these methods. Computational capacity of CA is equivalent to the universal Turing Machine. CA are multi-cellular systems in which uniform cells are allocated on lattice grid. Each cell has a finite number of states. The state transition is determined by the current state and the states of neighbor cells. Three mechanisms are required to implement CA in bacteria: (1) Sending and receiving signals between cells, (2) Sustaining the state, (3) Sensing input signals and changing the state following the state transition rules. To encode signals for the mechanism (1), we use small molecules inducing transcription. For the mechanism (2), the toggle switch circuit was employed to represent a finite number of states using gene expression. If one gene does express and the other does not, the state is 1, and vice versa, 0. For the mechanism (3), the state transition functions were implemented as logic gates using transcriptional regulatory proteins which bind to specific signal molecules (chemicals). In this paper, we applied this method to in vivo implementation of one-dimensional CA and corroborated whether it behaves correctly. In principle, this method can be applied to any dimensional CA by employing more signal molecules Permission to make digital or hard copies of all or part of this work for to construct more complex logic gate. Furthermore, we succeeded to execute one step calculation of one-dimensional CA in vivo in a laboratory experiment.
FACTORS OF JACOBIANS AND ISOTRIVIAL ELLIPTIC SURFACES

We show that the rank of the Mordell-Weil group of an isotrivial elliptic surface over C(t) can be calculated as the number of isogeny factors which are elliptic curves in the jacobian of the cyclic cover of a projective line associated to the elliptic surface. We illustrate this method by calculating the ranks in several examples, some of which recover already known results, and discuss relation between open questions on factors of jacobians and elliptic surfaces.