Miracle-dz/UniFAR-FTUs huggingface dataset:
Lathe: light-Weight Keyword Query Processing over Multiple Databases

We present a new R-KwS system called Lathe , which, is able to efﬁ-ciently deal with such conditions. Lathe is based on a probabilistic model and principled strategies which allow pruning unlike candidate solutions for a key-word query very early in the process. As a result, the system is able to produce accurate answers very quickly in comparison to current systems. Lathe is able to handle many distinct databases by trying a same query over multiple different target databases at once, and providing answers for all those databases that have an answer to the query.
Understanding Semi-structured Merge Conflict Characteristics in Open-Source Java Projects (Journal-First Abstract)

In a collaborative development environment, tasks are commonly assigned to developers working independent from each other. As a result, when trying to integrate these contributions, one might have to deal with conflicting changes. Such conflicts might be detected when merging contributions (merge conflicts), when building the system (build conflicts), or when running tests (semantic conflicts). Regarding such conflicts, previous studies show that they occur frequently, and impair developers' productivity, as understanding and solving them is a demanding and tedious task that might introduce defects. However, despite the existing evidence in the literature, the structure of changes that lead to conflicts has not been studied yet. Understanding the underlying structure of conflicts, and the involved syntactic language elements, might shed light on how to better avoid them. For example, awareness tools that inform users about ongoing parallel changes such as Syde and Palantír can benefit from knowing the most common conflict patterns to become more efficient. With that aim, in this paper we focus on understanding the underlying structure of merge conflicts.
Insights into the Etiology of Mammalian Neural Tube Closure Defects from Developmental, Genetic and Evolutionary Studies

The human neural tube defects (NTD), anencephaly, spina bifida and craniorachischisis, originate from a failure of the embryonic neural tube to close. Human NTD are relatively common and both complex and heterogeneous in genetic origin, but the genetic variants and developmental mechanisms are largely unknown. Here we review the numerous studies, mainly in mice, of normal neural tube closure, the mechanisms of failure caused by specific gene mutations, and the evolution of the vertebrate cranial neural tube and its genetic processes, seeking insights into the etiology of human NTD. We find evidence of many regions along the anterior–posterior axis each differing in some aspect of neural tube closure—morphology, cell behavior, specific genes required—and conclude that the etiology of NTD is likely to be partly specific to the anterior–posterior location of the defect and also genetically heterogeneous. We revisit the hypotheses explaining the excess of females among cranial NTD cases in mice and humans and new developments in understanding the role of the folate pathway in NTD. Finally, we demonstrate that evidence from mouse mutants strongly supports the search for digenic or oligogenic etiology in human NTD of all types.
Visual-Based Vehicle Speed Acquisition Algorithm

With the development of automotive industry and transportation industry, intelligent information processing becomes a global issue. In the near future, unmanned vehicle will be widely used the driving data of which needs monitoring carefully. The data of vehicle speed is important for analyzing the driving conditions and predict the danger of traffic accidents. When the road construction department judges a section of road as accident-prone areas, monitoring device will be installed to monitor the driving conditions. The algorithm proposed in this paper is used to extract vehicle speed from video. Gray matching method is used to lock the target vehicle. Weather the shooting device is drone or the installed monitoring device, the vehicle could be extracted with the video and will be tracked. The computing unit stalled in the shooting device will calculate the speed of the target vehicle based on frame difference. According to vehicle dynamics, the obtained vehicle speed could be used to calculate the condition of both vehicle and driver. The rolling resistance coefficient and air resistance can be calculated with the change of the speed. In the future, this technology will be used to detect the condition of each smart car on a specific road section. This algorithm provides a new way to obtain the vehicle speed and continuously monitors the vehicle conditions in a section of road. With the progress of visual recognition technology, speed recognition accuracy will greatly improve. During our study, the shooting device is installed on the flyover to record the track of the vehicle. The video is framed and grayed to obtain the vehicle speed. Compared to the actual speed, the error of the vehicle speed calculated with this algorithm is below 11.2%.
Correction: Biphasic targeting and cleavage furrow ingression directed by the tail of a myosin II

Vol. 191, No. 7, December 27, 2010. Pages [1333–1350][1]. After publication of the paper, the authors discovered an error in figure preparation. In [Fig. 3 B][2] of the original manuscript, the authors used the same mlc-11 GFP channel kymograph in both the mlc1-11 (left) and iqg1Δ (right) panels
Heterogeneous distribution of doublecortin‐expressing cells surrounding the rostral migratory stream in the juvenile mouse

In the postnatal mammalian brain, neural stem cells of the ventricular–subventricular zone continue to generate doublecortin (Dcx)‐expressing immature neurons. Throughout life, these immature neurons migrate to the olfactory bulb through the rostral migratory stream (RMS). In this study, we investigated the distribution of these putative immature neurons using enhanced green fluorescent protein (EGFP) expression in the area surrounding the RMS of the juvenile Dcx‐EGFP mice. Through the combined use of an optical clearing reagent (a 2,2′‐thiodiethanol solution) and two‐photon microscopy, we visualized three‐dimensionally the EGFP‐positive cells in the entire RMS and its surroundings. The resulting wide‐field and high‐definition images along with computational image processing methods developed in this study were used to comprehensively determine the position of the EGFP‐positive cells. Our findings revealed that the EGFP‐positive cells were heterogeneously distributed in the area surrounding the RMS. In addition, the orientation patterns of the leading process of these cells, which displayed the morphology of migrating immature neurons, differed depending on their location. These novel results provide highly precise morphological information for immature neurons and suggest that a portion of immature neurons may be detached from the RMS and migrate in various directions.
Is This Class Thread-Safe? Inferring Documentation using Graph-Based Learning

Thread-safe classes are pervasive in concurrent, object-oriented software. However, many classes lack documentation regarding their safety guarantees under multi-threaded usage. This lack of documentation forces developers who use a class in a concurrent program to either carefully inspect the implementation of the class, to conservatively synchronize all accesses to it, or to optimistically assume that the class is thread-safe. To overcome the lack of documentation, we present TSFinder, an approach to automatically classify classes as supposedly thread-safe or thread-unsafe. The key idea is to combine a lightweight static analysis that extracts a graph representation from classes with a graph-based classifier. After training the classifier with classes known to be thread-safe and thread-unsafe, it achieves an accuracy of 94.5% on previously unseen classes, enabling the approach to infer thread safety documentation with high confidence. The classifier takes about 3 seconds per class, i.e., it is efficient enough to infer documentation for many classes.
Arquitetura para Cocuradoria de Dados de Conhecimento Popular Integrados por meio de Linked Open Data

Bases de conhecimento popular estão se tornando essenciais para a preservação da cultura de uma região. No cenário Brasileiro, muitos museus e galerias não incorporam sistemas que exploram a inteligência coletiva de modo a auxiliar o registro de informações empíricas. Este trabalho tem como objetivo apresentar uma arquitetura para apoiar a cocuradoria de dados advindos do conhecimento popular. Nossa proposta também propicia a interconexão entre contribuições de visitantes com dados já dispostos em repositórios abertos na web (no formato Linked Open Data). A partir disso, espera-se conseguir o enriquecimento do patrimônio cultural de museus e suas galerias, beneficiando a comunidade com acesso a bases de conhecimento enriquecido e curado.
Tung Tree (Vernicia fordii, Hemsl.) Genome and Transcriptome Sequencing Reveals Co-Ordinate Up-Regulation of Fatty Acid &bgr;-Oxidation and Triacylglycerol Biosynthesis Pathways During Eleostearic Acid Accumulation in Seeds

The tung tree (Vernicia fordii) is one of only a few plant species that produces high oil-yielding seeds rich in α-eleostearic acid (α-ESA, 18:3Δ9cis, 11trans, 13trans), a conjugated trienoic fatty acid with valuable industrial and medical properties. Previous attempts have been made to engineer tung oil biosynthesis in transgenic oilseed crops, but these efforts have met with limited success. Here we present a high-quality genome assembly and developing seed transcriptomic data set for this species. Whole-genome shotgun sequencing generated 176 Gb of genome sequence data used to create a final assembled sequence 1,176,320 kb in size, with a scaffold N50 size of >474 kb, and containing approximately 47,000 protein-coding genes. Genomic and transcriptomic data revealed full-length candidate genes for most of the known and suspected reactions that are necessary for fatty acid desaturation/conjugation, acyl editing and triacylglycerol biosynthesis. Seed transcriptomic analyses also revealed features unique to tung tree, including unusual transcriptional profiles of fatty acid biosynthetic genes, and co-ordinated (and seemingly paradoxical) simultaneous up-regulation of both fatty acid β-oxidation and triacylglycerol biosynthesis in mid-development seeds. The precise temporal control of the expression patterns for these two pathways may account for α-ESA enrichment in tung seeds, while controlling the levels of potentially toxic by-products. Deeper understanding of these processes may open doors to the design of engineered oilseeds containing high levels of α-ESA.
Spindler: a framework for parametric analysis and detection of spindles in EEG with application to sleep spindles

Objective. EEG spindles, narrow-band oscillatory signal bursts, are widely-studied biomarkers of subject state and neurological function. Most existing methods for spindle detection select algorithm parameters by optimizing agreement with expert labels. We propose a new framework for selecting algorithm parameters based on stability of spindle properties and elucidate the dependence of these properties on parameter selection for several algorithms. Approach. To demonstrate this approach we developed a new algorithm (Spindler) that decomposes the signal using matching pursuit with Gabor atoms and computes the spindles for each point in a fine grid of parameter values. After computing characteristic surfaces as a function of parameters, Spindler selects algorithm parameters based on the stability of characteristic surface geometry. Main results. Spindler performs well relative to several common supervised and unsupervised EEG sleep spindle detection methods. Spindler is available as an open-source MATLAB toolbox (https://github.com/VisLab/EEG-Spindles). In addition to Spindler, the toolbox provides implementations of several other spindle detection algorithms as well as standardized methods for matching ground truth to predictions and a framework for understanding algorithm parameter surfaces. Significance. This work demonstrates that parameter selection based on physical constraints rather than labelled data can provide effective, fully-automated, unsupervised spindle detection. This work also exposes the dangers of applying cross-validation without considering the dependence of spindle properties on parameters. Parameters selected to optimize one performance metric or matching method are not optimized for others. Furthermore, elucidation of the stability of predicted indicators with respect to algorithm parameter selection is critical to practical application of these algorithms.
Migrating towards microservices: migration and architecture smells

Migrating to microservices is an error-prone process with deep pitfalls resulting in high costs for mistakes. Microservices is a relatively new architectural style, resulting in the lack of general guidelines for migrating monoliths towards microservices. We present 9 common pitfalls in terms of bad smells with their potential solutions. Using these bad smells, pitfalls can be identified and corrected in the migration process.
Immunotherapeutic maintenance treatment with toll-like receptor 9 agonist lefitolimod in patients with extensive-stage small-cell lung cancer: results from the exploratory, controlled, randomized, international phase II IMPULSE study

Abstract Background The immune surveillance reactivator lefitolimod (MGN1703), a DNA-based TLR9 agonist, might foster innate and adaptive immune response and thus improve immune-mediated control of residual cancer disease. The IMPULSE phase II study evaluated the efficacy and safety of lefitolimod as maintenance treatment in extensive-stage small-cell lung cancer (ES-SCLC) after objective response to first-line chemotherapy, an indication with a high unmet medical need and stagnant treatment improvement in the last decades. Patients and methods 103 patients with ES-SCLC and objective tumor response (as per RECIST 1.1) following four cycles of platinum-based first-line induction therapy were randomized to receive either lefitolimod maintenance therapy or local standard of care at a ratio of 3 : 2 until progression or unacceptable toxicity. Results From 103 patients enrolled, 62 were randomized to lefitolimod, 41 to the control arm. Patient demographics and response patterns to first-line therapy were balanced. Lefitolimod exhibited a favorable safety profile and pharmacodynamic assessment confirmed the mode-of-action showing a clear activation of monocytes and production of interferon-gamma-induced protein 10 (IP-10). While in the intent-to-treat (ITT) population no relevant effect of lefitolimod on progression-free and overall survival (OS) could be observed, two predefined patient subgroups indicated promising results, favoring lefitolimod with respect to OS: in patients with a low frequency of activated CD86+ B cells (hazard ratio, HR 0.53, 95% CI: 0.26–1.08; n = 38 of 88 analyzed) and in patients with reported chronic obstructive pulmonary disease (COPD) (HR 0.48, 95% CI: 0.20–1.17, n = 25 of 103). Conclusions The IMPULSE study showed no relevant effect of lefitolimod on the main efficacy end point OS in the ITT, but (1) the expected pharmacodynamic response to lefitolimod, (2) positive OS efficacy signals in two predefined subgroups and (3) a favorable safety profile. These data support further exploration of lefitolimod in SCLC.
Total Synthesis of Pulmonarin B and Design of Brominated Phenylacetic Acid/Tacrine Hybrids: Marine Pharmacophore Inspired Discovery of New ChE and Aβ Aggregation Inhibitors

A marine natural product, pulmonarin B (1), and a series of related tacrine hybrid analogues were synthesized and evaluated as cholinesterase (ChE) inhibitors. The in vitro ChE assay results revealed that 1 showed moderate dual acetylcholinesterase (AChE)/ butyrylcholinesterase (BChE) inhibitory activity, while the hybrid 12j proved to be the most potent dual inhibitor among the designed derivatives, being almost as active as tacrine. Molecular modeling studies together with kinetic analysis suggested that 12j interacted with both the catalytic active site and peripheral anionic site of AChE. Compounds 1 and 12j could also inhibit self-induced and AChE-induced Aβ aggregation. In addition, the cell-based assay against the human hepatoma cell line (HepG2) revealed that 1 and 12j did not show significant hepatotoxicity compared with tacrine and donepezil. Taken together, the present study confirmed that compound 1 was a potential anti-Alzheimer’s disease (AD) hit, and 12j could be highlighted as a multifunctional lead compound for anti-AD drug development.
A Unified Lattice Model and Framework for Purity Analyses

Analyzing methods in object-oriented programs whether they are side-effect free and also deterministic, i.e., mathematically pure, has been the target of extensive research. Identifying such methods helps to find code smells and security related issues, and also helps analyses detecting concurrency bugs. Pure methods are also used by formal verification approaches as the foundations for specifications and proving the pureness is necessary to ensure correct specifications. However, so far no common terminology exists which describes the purity of methods. Furthermore, some terms (e.g., pure or side-effect free) are also used inconsistently. Further, all current approaches only report selected purity information making them only suitable for a smaller subset of the potential use cases. In this paper, we present a fine-grained unified lattice model which puts the purity levels found in the literature into relation and which adds a new level that generalizes existing definitions. We have also implemented a scalable, modularized purity analysis which produces significantly more precise results for real-world programs than the best-performing related work. The analysis shows that all defined levels are found in real-world projects.
Feedback stabilisation of an Euler–Bernoulli beam with the boundary time-delay disturbance

ABSTRACT In this paper, we consider the feedback stabilisation of an Euler–Bernoulli beam with the boundary time-delay disturbance. Due to unknown time-delay coefficient, the system might be exponentially increasing at the lack of control. We design the feedback control law based on Lyapunov function method. Different from usual use of Lyapunov function method, our approach is to combine the construction of Lyapunov functionals with the controller design, which will guarantee the system energy function decays exponentially. In this procedure, we deduce the inequality equations satisfied by the system parameters. We prove the well-posedness of the corresponding closed-loop system by using semigroup theory and the inequality equations are solvable. Moreover, the exponential decay rate of the system is estimated. In addition, some numerical simulations are also presented to support the obtained results.
Faster processing of moving compared to flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion

When the brain has determined the position of a moving object, due to anatomical and processing delays, the object will have already moved to a new location. Given the statistical regularities present in natural motion, the brain may have acquired compensatory mechanisms to minimize the mismatch between the perceived and the real position of a moving object. A well-known visual illusion — the flash lag effect — points towards such a possibility. Although many psychophysical models have been suggested to explain this illusion, their predictions have not been tested at the neural level, particularly in a species of animal known to perceive the illusion. Towards this, we recorded neural responses to flashed and moving bars from primary visual cortex (V1) of awake, fixating macaque monkeys. We found that the response latency to moving bars of varying speed, motion direction and luminance was shorter than that to flashes, in a manner that is consistent with psychophysical results. At the level of V1, our results support the differential latency model positing that flashed and moving bars have different latencies. As we found a neural correlate of the illusion in passively fixating monkeys, our results also suggest that judging the instantaneous position of the moving bar at the time of flash — as required by the postdiction/motion-biasing model — may not be necessary for observing a neural correlate of the illusion. Our results also suggest that the brain may have evolved mechanisms to process moving stimuli faster and closer to real time compared with briefly appearing stationary stimuli. New and Noteworthy We report several observations in awake macaque V1 that provide support for the differential latency model of the flash lag illusion. We find that the equal latency of flash and moving stimuli as assumed by motion integration/postdiction models does not hold in V1. We show that in macaque V1, motion processing latency depends on stimulus luminance, speed and motion direction in a manner consistent with several psychophysical properties of the flash lag illusion.
Android Testing via Synthetic Symbolic Execution

Symbolic execution of Android applications is challenging as it involves either building a customized VM for Android or modeling the Android libraries. Since the Android Runtime evolves from one version to another, building a high-fidelity symbolic execution engine involves modeling the effect of the libraries and their evolved versions. Without simulating the behavior of Android libraries, path divergence may occur due to constraint loss when the symbolic values flow into Android framework and these values later affect the subsequent path taken. Previous works such as JPF-Android have relied on the modeling of execution environment such as libraries. In this work, we build a dynamic symbolic execution engine for Android apps, without any manual modeling of execution environment. Environment (or library) dependent control flow decisions in the application will trigger an on-demand program synthesis step to automatically deduce a representation of the library. This representation is refined on-the-fly by running the corresponding library multiple times. The overarching goal of the refinement is to enhance behavioral coverage and to alleviate the path divergence problem during symbolic execution. Moreover, our library synthesis can be made context-specific. Compared to traditional synthesis approaches which aim to synthesize the complete library code, our context-specific synthesis engine can generate more precise expressions for a given context. The evaluation of our dynamic symbolic execution engine, built on top of JDART, shows that the library models obtained from program synthesis are often more accurate than the semi-manual models in JPF-Android. Furthermore, our symbolic execution engine could reach more branch targets, as compared to using the JPF-Android models.