Miracle-dz/UniFAR-FTUs huggingface dataset:
A change-aware development environment by recording editing operations of source code

Understanding a program and its evolution is not satisfied only by looking at a current snapshot of its source code. Thus, a developer often examines a sequence of its snapshots stored in repositories of versioning systems, and identifies differences between two successive snapshots. Unfortunately, such differences do not represent individual changes of the source code. This paper proposes a mechanism for recording all editing operations a developer has applied to source code on an integrated development environment. The paper also shows a running implementation of the mechanism built as an Eclipse plug-in, which is called OperationRecorder. The experimental results with a small-scale program substantiate that it has a practical use from the viewpoint of its performance.
A Matching Algorithm for Selecting Web Services Based on Non-Functional Features

Searching for a Web service that meets the user requirements can be a complex task especially when the system starts to scale up by increasing the number of Web services, w, in the UDDI registry and by enlarging the number of QoS features (f) by which each Web service is described. This can be perceived as the commonly known nearest neighbor search problem, which typically imposes a time or storage complexity that is exponential in f. In this work, we present a new algorithm (wsSVD) that is founded on the algebraic matrix operation called Singular Value Decomposition (SVD). The basic idea is to encode the features of each Web service by a single value using the SVD. When a user seeks a Web service based on some specific requirements, these requirements get encoded by a single value using the same algorithm, and the matching process takes place in order to find the closest Web service that fulfills the user requirements. Our experiments show that the wsSVD algorithm performs and scales up well in comparison with other matching algorithms.
Integration of Stem Cell to Chondrocyte-Derived Cartilage Matrix in Healthy and Osteoarthritic States in the Presence of Hydroxyapatite Nanoparticles

We investigated the effectiveness of integrating tissue engineered cartilage derived from human bone marrow derived stem cells (HBMSCs) to healthy as well as osteoarthritic cartilage mimics using hydroxyapatite (HA) nanoparticles immersed within a hydrogel substrate. Healthy and diseased engineered cartilage from human chondrocytes (cultured in agar gels) were integrated with human bone marrow stem cell (HBMSC)-derived cartilaginous engineered matrix with and without HA, and evaluated after 28 days of growth. HBMSCs were seeded within photopolymerizable poly (ethylene glycol) diacrylate (PEGDA) hydrogels. In addition, we also conducted a preliminary in vivo evaluation of cartilage repair in rabbit knee chondral defects treated with subchondral bone microfracture and cell-free PEGDA with and without HA. Under in vitro conditions, the interfacial shear strength between tissue engineered cartilage derived from HBMSCs and osteoarthritic chondrocytes was significantly higher (p < 0.05) when HA nanoparticles were incorporated within the HBMSC culture system. Histological evidence confirmed a distinct spatial transition zone, rich in calcium phosphate deposits. Assessment of explanted rabbit knees by histology demonstrated that cellularity within the repair tissues that had filled the defects were of significantly higher number (p < 0.05) when HA was used. HA nanoparticles play an important role in treating chondral defects when osteoarthritis is a co-morbidity. We speculate that the calcified layer formation at the interface in the osteoarthritic environment in the presence of HA is likely to have attributed to higher interfacial strength found in vitro. From an in vivo standpoint, the presence of HA promoted cellularity in the tissues that subsequently filled the chondral defects. This higher presence of cells can be considered important in the context of accelerating long-term cartilage remodeling. We conclude that HA nanoparticles play an important role in engineered to native cartilage integration and cellular processes.
2D Face Recognition System Based on Selected Gabor Filters and Linear Discriminant Analysis LDA

In this paper, we present a new approach for face recognition system. The method is based on 2D face image features using subset of non-correlated and Orthogonal Gabor Filters instead of using the whole Gabor Filter Bank, then compressing the output feature vector using Linear Discriminant Analysis (LDA). The face image has been enhanced using multi stage image processing technique to normalize it and compensate for illumination variation. Experimental results show that the proposed system is effective for both dimension reduction and good recognition performance when compared to the complete Gabor filter bank. The system has been tested using CASIA, ORL and Cropped YaleB 2D face images Databases and achieved average recognition rate of 98.9 %.
Workload dependent IO scheduling for fairness and efficiency in shared storage systems

Supporting QoS control mechanisms in shared storage arrays is constrained by the well-justified fear of impacting the system efficiency. This motivates our study of the trade off between fairness and efficiency in shared storage systems. We propose two adaptations that can be applied to existing IO scheduling mechanisms: the concurrency bound and the batch size. Although these knobs are well known, their impact on system performance and automatic adaptation based on current workload characteristics have not been studied before. Using synthetic benchmarks and trace workloads, we show that the adaptive proportional share algorithm achieves over 90% IO efficiency while maintaining the specified QoS requirements.
High-speed point cloud matching algorithm for medical volume images using 3D Voronoi diagram

Several respiratory diseases, such as COPD and asthma, requires periodical checkups and past data comparison. While this kind of analysis is usually done by a medical expert, it depends greatly on the medical expertise and the image quality. Image registration, a technique which compares images volumes automatically using predefined computational algorithms, is a great tool to assist on diagnosis and disease surveillance. Most studies analyze the registration on 3D CT images slice-by-slice. However, by segmenting a 3D point clouds from the 3D CT volumes, it is possible to analyze the data in different and more accurate ways. This paper proposes a high speed algorithm improvement that calculates the rigid registration between two point clouds, adapting the Iterative Closest Point (ICP) algorithm to use 3D Voronoi diagrams for point correspondence determination, reducing the processing time greatly. A benchmark performance test is done with a point-by-point variation of the algorithm, showing that the proposed algorithm yield the same results with a considerable processing time reduction.
Learning basic block scheduling heuristics from optimal data

Instruction scheduling is an important step for improving the performance of object code produced by a compiler. The basic block instruction scheduling problem is to find a minimum length schedule for a basic block-a straight-line sequence of code with a single entry point and a single exit point-subject to precedence, latency, and resource constraints. Solving the problem exactly is known to be difficult, and most compilers use a greedy list scheduling algorithm coupled with a heuristic. The heuristic is usually hand-crafted, a potentially time-consuming process. In contrast, we present a study on automatically learning good heuristics using techniques from machine learning. In our study, a recently proposed optimal basic block scheduler was used to generate the machine learning training data. A decision tree learning algorithm was then used to induce a simple heuristic from the training data. The automatically constructed decision tree heuristic was compared against a popular criticalpath heuristic on the SPEC 2000 benchmarks. On this benchmark suite, the decision tree heuristic reduced the number of basic blocks that were not optimally scheduled by up to 55% compared to the critical-path heuristic, and gave improved performance guarantees in terms of the worst-case factor from optimality.
Interrelations among pressure–volume curve traits across species and water availability gradients

Pressure-volume (P-V) curves for leaves or terminal shoots summarize leaf-level responses to increasing water deficit. P-V curve traits and field-measured shoot xylem pressures were characterized across 62 species from four sites differing in rainfall and soil phosphorus. Within-species variation in the measured traits was small relative to differences among species and between environments. P-V curve traits tended to differ with site rainfall but not with soil phosphorus. Turgor loss points (TLPs) varied widely and averaged more negative in species from lower-rainfall sites. Differences between species in TLP were driven mainly by differences in solute potential, rather than by differences in cell wall elasticity. Among species at individual sites, species seemed to vary in leaf-response strategy reflected in TLP independently from water-uptake strategy reflected in predawn xylem pressures and in xylem pressure drop from predawn to midday.
YARP: Yet Another Robot Platform

We describe YARP, Yet Another Robot Platform, an open-source project that encapsulates lessons from our experience in building humanoid robots. The goal of YARP is to minimize the effort devoted to infrastructure-level software development by facilitating code reuse, modularity and so maximize research-level development and collaboration. Humanoid robotics is a “bleeding edge” field of research, with constant flux in sensors, actuators, and processors. Code reuse and maintenance is therefore a significant challenge. We describe the main problems we faced and the solutions we adopted. In short, the main features of YARP include support for inter-process communication, image processing as well as a class hierarchy to ease code reuse across different hardware platforms. YARP is currently used and tested on Windows, Linux and QNX6 which are common operating systems used in robotics.
Analysis of downstream effectors of p53 on cell growth arrest and apoptosis induced by a temperature-sensitive Val138 mutant.

To elucidate the mechanism for cell growth arrest in relation to apoptosis mediated by the p53 gene, I studied two p53-null human cancer cell lines (K562 and Jurkat) carrying a human p53 temperature sensitive (ts) mutant (p53138val). The cell growth in the newly established K562 cells carrying the ts mutant was arrested in G0/G1 at the permissive temperature (32.5 degrees C) , at least in part, due to induction of p21/waf1. In apoptosis-induced Jurkat cells upon temperature shift-down, a lower level of p21 induction relative to that of MDM2 was observed in comparison with that in K562 cells. Meanwhile, levels of bax and bcl-2 expression were relatively constant upon temperature shift-down in both cell lines. Studies on the phosphorylation pattern of Rb family proteins, and results of gel-shift and antibody super-shift assays showed the accumulation of Rb/E2F complexes in growth-arrested K562 cells, but no such phenomenon was observed in Jurkat cells. Taken together, the results are consistent with the idea that a higher level of p21 expression and its subsequent Rb/E2F complex formation played an important role in the growth arrest of K562 cells.
Pressor Responses to Ephedrine Are Mediated by a Direct Mechanism in the Rat

The mechanism of the pressor response to ephedrine is controversial. In the present study. i.v. injections of ephedrine increased systemic and pulmonary arterial pressure, and i.a. injections decreased hindlimb blood flow in a dose-related manner. Responses to ephedrine were inhibited by α-receptor blocking agents and were not attenuated by blockade of the norepinephrine reuptake transporter (NET) or by catecholamine depletion using reserpine or a combination of reserpine and α-methyl-p-tyrosine, whereas responses to tyramine and amphetamine were inhibited by these treatments. The magnitude of the pressor response to ephedrine was similar in anesthetized and conscious rats. Tachyphylaxis developed to pressor responses to ephedrine and amphetamine with sequential injections; however, ephedrine tachyphylaxis differed in that subsequent responses to α-receptor agonists were attenuated. These results suggest that the systemic and pulmonary pressor and hindlimb vasoconstrictor responses to ephedrine are mediated by direct action on α-adrenergic receptors and that the release of norepinephrine from adrenergic terminals plays no significant role. These results provide support for the hypothesis that responses to ephedrine are directly mediated in the intact rat, whereas responses to amphetamine are mediated in a large part by the release of norepinephrine from adrenergic terminals.
Maturity of Operational Procurement in the Construction Industry: A Business/IT-Alignment Perspective

From the article: "Project execution in the construction industry faces major challenges, e.g. difficulty in coordination and cooperation. Operational procurement during project execution is no exception. In this paper we construct a maturity model, based on earlier work, consisting of six dimensions (goal, control, process, organization, information, technology) and five maturity stages (transactional-oriented, commercial-oriented, coordination, internal-optimized, external-optimized). The model can be used to determine the level of procurement maturity for each of the dimensions, and for the determination of a strategy for growth in the construction industry. With input from a major construction firm in the Netherlands, through simulating tooling, the model is evaluated for its contribution to growth in operational excellence. Results of the simulation show support for a relation between maturity growth and increased operational excellence. " Recommended Citation Xing, Xiaochun; Versendaal, Johan; van den Akker, Marjan; and De Bevere, Bastiaan, "Maturity of Operational Procurement in the Construction Industry: A Business/IT-Alignment Perspective" (2011). BLED 2011 Proceedings. Paper 22. http://aisel.aisnet. org/bled2011/22 Affiliation: Xing Xiaochun - Swets Information Services, Netherlands; Johan Versendaal - Utrecht University, Netherlands; HU University of Applied Sciences, Netherlands; Marjan van den Akker - Utrecht University, Netherlands; Bastiaan De Bevere - Ballast Nedam, Netherlands.
Development of PSMA inhibitors for molecular imaging and radio-guided surgery of prostate cancer

Due to the high and consistent expression of the prostate-specific membrane antigen (PSMA) and the high accessibility as a cell-membrane protein it represents an excellent molecular target for both diagnostic imaging and therapy of prostate cancer (PCa). The presented thesis focused on the development and (pre)clinical evaluation of urea-based PSMA inhibitors for the diagnosis of PCa, labeled either with 18F for PET or with 99mTc for SPECT imaging, as well as for radioguided surgery of PCa patients.
Macrophage polarization in the maculae of age‐related macular degeneration: A pilot study

Macrophages can be polarized to exhibit either pro‐inflammatory M1 or pro‐angiogenic M2 phenotypes, but have high phenotypic plasticity. This pilot study investigated macrophage polarization in the macular retina and choroid of age‐related macular degeneration (AMD) and non‐AMD subjects, as well as in AMD choroidal neovascular membranes (CNVM). All specimens were evaluated for routine histopathology. Quantitative real‐time polymerase chain reaction for representative M1 (CXCL11) and M2 (CCL22) transcripts were performed on macular choroidal trephines (MCT) of 19 AMD and nine non‐AMD eye bank eyes, on the microdissected macular retinal cells from the archived slides of five geographic atrophic AMD, five exudative/neovascular AMD, and eight normal autopsied eyes, and on microdissected inflammatory cells from two surgically removed CNVM that did not respond to anti‐vascular endothelial growth factor (VEGF) therapy. High M2‐chemokine transcript and a low ratio of M1 to M2 chemokine transcript were found in aging non‐AMD MCT. Advanced AMD maculae had a higher M1 to M2 chemokine transcript ratio compared to normal autopsied eyes. Macrophages in the two CNVM of patients unresponsive to anti‐VEGF therapy were polarized toward either M1 or M2 phenotypes. The number of M2 macrophages was increased compared to M1 macrophages in normal aging eyes. A pathological shift of macrophage polarization may play a potential role in AMD pathogenesis.
Bevacizumab-Induced Transient Remodeling of the Vasculature in Neuroblastoma Xenografts Results in Improved Delivery and Efficacy of Systemically Administered Chemotherapy

Purpose: Dysfunctional tumor vessels can be a significant barrier to effective cancer therapy. However, increasing evidence suggests that vascular endothelial growth factor (VEGF) inhibition can effect transient “normalization” of the tumor vasculature, thereby improving tumor perfusion and, consequently, delivery of systemic chemotherapy. We sought to examine temporal changes in tumor vascular function in response to the anti-VEGF antibody, bevacizumab. Experimental Design: Established orthotopic neuroblastoma xenografts treated with bevacizumab were evaluated at serial time points for treatment-associated changes in intratumoral vascular physiology, penetration of systemically administered chemotherapy, and efficacy of combination therapy. Results: After a single bevacizumab dose, a progressive decrease in tumor microvessel density to <30% of control was observed within 7 days. Assessment of the tumor microenvironment revealed a rapid, sustained decrease in both tumor vessel permeability and tumor interstitial fluid pressure, whereas intratumoral perfusion, as assessed by contrast-enhanced ultrasonography, was improved, although this latter change abated by 1 week. Intratumoral drug delivery mirrored these changes; penetration of chemotherapy was improved by as much as 81% when given 1 to 3 days after bevacizumab, compared with when both drugs were given concomitantly, or 7 days apart. Finally, administering topotecan to tumor-bearing mice 3 days after bevacizumab resulted in greater tumor growth inhibition (36% of control size) than with monotherapy (88% bevacizumab, 54% topotecan) or concomitant administration of the two drugs (44%). Conclusions: Bevacizumab-mediated VEGF blockade effects alterations in tumor vessel physiology that allow improved delivery and efficacy of chemotherapy, although careful consideration of drug scheduling is required to optimize antitumor activity.
Full body motion adaption based on task-space distance meshes

This paper presents a novel robot pose measure for human movement imitation based entirely on the Euclidean distance information between any two links of a robot and any link and object in the robot's environment in a Cartesian task space. A Hidden Markov Model is used to encode the spatio-temporal information of multiple demonstrations. In combination with Gaussian Mixture Regression for extracting the important task properties, feasible full-body motion adaption can be achieved. The method is suited for use with a humanoid robot by considering additional constraints like balance control and collision avoidance. In order to tackle modeling errors occurring due to the human movement demonstration and the robotic reproduction, a manipulability based weighting scheme is proposed. Complexity reduction of the otherwise redundant pose measure is performed based upon a mechanical analogy of an interconnected spring system. Experiments are conducted using a HRP-4 robot and display the applicability of the presented methods for robotic full-body motion imitation tasks.
Runge-Kutta Starters for Multistep Methods

Multistep Runge-Kutta-like formulas which enable a multmtep method to start or restart at a high order after lust one Runge-Kutta (RK) step are presented. These formulas greatly improve the efficiency of mnltistep methods in a situation m which they were previously out performed by RK methods-i e. , m which there are problems with frequent dlscontinmties or sudden large increases in derivatives, all of which cause an automatic program to reduce order and step size suddenly.
Bivariate simplex B-splines: a new paradigm

A construction of bivariate splines is described, based on a new concept of higher degree Delaunay configurations. The crux of this construction is that knot-sets for simplex B-splines are selected by considering groups of "nearby" knots. The new approach gives rise to a natural generalization of univariate splines in that the linear span of this collection of B-splines forms a space which is analogous to the classical univariate splines. This new spline space depends uniquely and in a local way on the prescribed knot locations, and there is no need to use auxiliary or perturbed knots as in some earlier constructions.
Modeling and Analyzing MAPE-K Feedback Loops for Self-Adaptation

The MAPE-K (Monitor-Analyze-Plan-Execute over a shared Knowledge) feedback loop is the most influential reference control model for autonomic and self-adaptive systems. This paper presents a conceptual and methodological framework for formal modeling, validating, and verifying distributed self-adaptive systems. We show how MAPE-K loops for self adaptation can be naturally specified in an abstract stateful language like Abstract State Machines. In particular, we exploit the concept of multi-agent Abstract State Machines to specify decentralized adaptation control by using MAPE computations. We support techniques for validating and verifying adaptation scenarios, and getting feedback of the correctness of the adaptation logic as implemented by the MAPE-K loops. In particular, a verification technique based on meta-properties is proposed to allow discovering unwanted interferences between MAPE-K loops at the early stages of the system design. As a proof-of concepts, we model and analyze a traffic monitoring system.
Efficacy of a cell extract from Actinobacillus (Haemophilus) pleuropneumoniae serotype 1 against disease in swine

We partially characterized a cell extract (CE) from Actinobacillus pleuropneumoniae serotype 1 and used the CE to test the efficacy of secreted proteins against disease. Secreted products from 4-h culture supernatants were precipitated with 20% polyethylene glycol. Analysis of the CE indicated the presence of protein, endotoxin, and carbohydrate. Hemolytic activity to bovine erythrocytes and cytotoxic activity to porcine mononuclear leukocytes was also demonstrated. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of the CE from a 4-h culture showed a major band at 110 kilodaltons (kDa), while a CE of a 26-h culture indicated the presence of a number of additional proteins, including the 110-kDa protein. The 110-kDa protein was also identified as a glycoprotein by periodic acid-Schiff and silver staining. A single band precipitated against convalescent-phase pig antiserum when the polyethylene glycol precipitate was used in an Ouchterlony plate. Vaccination with CE conferred greater protection against challenge with the homologous serotype than either a commercial bacterin or an outer membrane protein vaccine. Hemolysin-neutralizing titers were higher both pre- and postchallenge in the group vaccinated with the CE compared with in all other groups. We believe that this demonstrates the importance of secreted factors in protection against disease and suggests that the 110-kDa protein is an important immunogen.