Miracle-dz/UniFAR-FTUs huggingface dataset:
Handling test length bloat

The length of test cases is a little investigated topic in search‐based test generation for object‐oriented software, where test cases are sequences of method calls. Although intuitively longer tests can achieve higher overall code coverage, there is always the threat of bloat – a complex phenomenon in evolutionary computation, where the length abnormally grows over time. In this paper, we show that bloat indeed also occurs in the context of test generation for object‐oriented software. We present different techniques to overcome the problem of length bloat, and evaluate all possible combinations of these techniques using different starting lengths for the search. Experiments on a set of difficult search targets, selected from several open source and industrial projects, show that controlling bloat with the appropriate techniques can significantly improve the search performance. Copyright © 2013 John Wiley & Sons, Ltd.
A general framework for constrained mesh parameterization

Parameterizing or flattening a triangle mesh is necessary for many applications in computer graphics and geometry. While mesh parameterization is a very popular research topic, the vast majority of the literature is focused on minimizing distortion or satisfying constraints related to certain applications such as texturing or quadrilateral remeshing. Certain downstream applications require adherence to more general, geometric constraints -- possibly at the cost of higher distortion. These geometric constraints include requirements such as certain vertices lie on some line or circle, or a planar curve or developable region keeps its shape during parameterization. We present a framework for enforcing such constraints, motivated by the As-Rigid-As-Possible parameterization method, and demonstrate its effectiveness through several examples.
Switching Behavior Constraint in the Heterogate Electron–Hole Bilayer Tunnel FET: The Combined Interplay Between Quantum Confinement Effects and Asymmetric Configurations

Switching behavior in electron-hole bilayer tunnel FETs is known to be unaffected by the subthreshold swing limitation of 60 mV/decade imposed by thermal injection, due to the band-to-band tunneling phenomena on which they rely. However, in this paper, we show that, once parasitic lateral tunneling processes are suppressed by means of heterogate configurations, a new physical limitation arises at the onset of tunneling in this type of transistors, resulting from the interplay between field-induced quantum confinement and asymmetric concentrations of electrons and holes inside the channel. We demonstrate that this limitation comes from the fact that, regardless of the band profile sharpness, the tunneling distance at subband alignment cannot be reduced beyond a certain limit, which we find to be dependent on the body thickness and the material properties.
Ginkgo Biloba Extract Protects Substantia Nigral Neurons from Apoptosis in PD Rat Model

Purpose: To investigate the apoptotic mechanism during the pathological process of Parkinson disease (PD) and explore the availability of Ginkgo biloba extract (EGb) to cure PD. Methods: Followed 6-OHDA injection stereotaxically to right side of substantia nigra pars compacta(SNc), at the date of 1, 7,14 and 21, we used biochemical, immunohistochemical, TUNEL and electron microscopic techniques to evaluate the level of apoptosis (TUNEL), monitor the degree of oxidative reaction (MDA.SOD), and to observe the change of ultrastructure of substantia nigra in the experimental PD models of rats (PD group), the EGb treatment group (EGb group) and the control group. Results: Contrast to the Control group, the number of apoptotic neurons and free radical level increased in the PD group and the EGb group, but the PD group surpassed the EGb group (p<0.05). In the PD group, the ultrastructure of substantia nigra exhibited the morphological characteristics of apoptosis from 1d to 21d. Conclusions: Free radical insult contributes to the pathological process of PD in rats. EGb may ameliorate the injury of substantia nigra through expiring free radicals during the pathological process of PD in rats.
DRAFT Version Robust trajectory tracking for a reversing tractor-trailer system

Tractor-trailer reversing is a classical non-linear control problem in which many of the solutions proposed in the literature perform poorly in the presence of real-world constraints such as steering angle, rate limits and lags. In this paper we describe a new method in which an inner loop controls the hitch-angle of the trailer creating a virtual articulated vehicle to which existing control techniques can be applied. We provide an analysis of the stability and convergence properties of this control approach, as well as experimental results which illustrate the robustness of this approach to model estimation errors, low-level control loop dynamics, and other disturbances introduced by, for example, state estimation errors.
Clustering genes with expression and beyond

Clustering over gene expression is now a popular computational analysis in biology. In general, the amount of expression can be measured by high‐throughput techniques over thousands of genes simultaneously. The expression dataset can be a large table (or matrix) with numerical values, each being specified by one gene and one sample, and needs computational methods to be analyzed. This review starts with surveying techniques of clustering genes by expression, classifying them into three types: hierarchical, partitional, and subspace clustering. Major methods of hierarchical and partitional clustering as well as a variety of algorithms for subspace clustering are extensively reviewed. Techniques for clustering over expression, however, are now well matured and their performance is limited due to the inevitable noisiness of the high‐throughput nature of expression data. We then extend the scope of this review further to clustering genes with recently emerging data, gene networks, and show graph partitioning approaches, such as spectral methods, for clustering genes by a network. Furthermore, advanced approaches of gene clustering now combine gene networks with expression. This setting corresponds to so‐called semi‐supervised clustering in machine learning, and approaches under this problem setting will be widely reviewed, classifying those approaches into three types. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 496–511 DOI: 10.1002/widm.41
Holding the Internet Accountable

Today’s IP network layer provides little to no protection against misconfiguration or malice. Despite some progress in improving the robustness and security of the IP layer, misconfigurations and attacks still occur frequently. We show how a network layer that provides accountability, i.e., the ability to associate each action with the responsible entity, provides a firm foundation for defenses against misconfiguration and malice. We present the design of a network layer that incorporates accountability called AIP (Accountable Internet Protocol) and show how its features—notably, its use of self-certifying addresses— can improve both source accountability (the ability to trace actions to a particular end host and stop that host from misbehaving) and control-plane accountability (the ability to pinpoint and prevent attacks on routing).
Novel Human Adenovirus Causing Nosocomial Epidemic Keratoconjunctivitis

ABSTRACT In 2000, we encountered cases of nosocomial infections with epidemic keratoconjunctivitis (EKC) at a university hospital in Kobe, in the western part of Japan. Two human adenovirus (HAdV) strains, Kobe-H and Kobe-S, were isolated from patients with nosocomial EKC infection. They were untypeable by existing neutralizing antisera; however, the isolate was neutralized with homologous antisera. We then encountered several cases of EKC due to nosocomial infections in eye clinics in different parts of Japan. A total of 80 HAdVs were isolated from patients with EKC at eight different hospitals. The partial hexon gene sequences of the isolates were determined and compared to those of the prototype strains of 51 serotypes. All isolates had identical partial hexon nucleotide sequences. Phylogenetic analysis classified these isolates into species of HAdV-D. The isolates showed 93.9 to 96.7% nucleotide identity with HAdV-D prototype strains, while all 32 HAdV-D prototype strains ranged from 93.2 to 99.2% identity. The sequences of the loop 2 and fiber knob regions from the representative strain, Kobe-H, were dissimilar in all prototype strains of 51 serotypes. We believe that this virus is a novel serotype of HAdV that causes EKC.
Bank Influence , Firm Performance and Survival

We extend the empirical literature by systematically investigating the impact of bank-influence on the firm performance and survival. Close bank-firm relationships which characterize the Japanese and German financial systems are often credited with reducing agency problems and improving monitoring of firm activities, thus improving firm performance and the chances of survival. Preliminary results reveal that bank influenced firms do indeed have higher survival rates than independent firms. However, firm growth appears to be independent of bank influence and negatively related to firm size.
New protocol for leg ulcer tissue classification from colour images

Measurement of wound healing status is very important for monitoring progress in individual patients. Tissue classification is a vital step in the development of an automatic measurement system for wound healing assessment. We present a new tissue classification protocol using the RGB (Red, Green and Blue) histogram distributions of pixel values from wound color images. These three histogram distributions (extracted features) were used as three two-dimensional (2D) input signals for classification. This protocol has been carried out using the KNN classifier and results show that the proposed protocol provides an extremely competent practical method for the classification of wound tissues.
From Spectra to Biophysical Insights: End-to-End Learning with a Biased Radiative Transfer Model

Advances in machine learning have boosted the use of Earth observation data for climate change research. Yet, the interpretability of machine-learned representations remains a challenge, particularly in understanding forests' biophysical reactions to climate change. Traditional methods in remote sensing that invert radiative transfer models (RTMs) to retrieve biophysical variables from spectral data often fail to account for biases inherent in the RTM, especially for complex forests. We propose to integrate RTMs into an auto-encoder architecture, creating an end-to-end learning approach. Our method not only corrects biases in RTMs but also outperforms traditional techniques for variable retrieval like neural network regression. Furthermore, our framework has potential generally for inverting biased physical models. The code is available on https://github.com/yihshe/ai-refined-rtm.git.
DISC: dynamic instruction stream computer

The Dynamic Instruction Stream Computer is a novel computer architecture which addresses many of the problems present in real-time systems. The DISC operates by allowing multiple instruction streams (ISs), representing different processes to run concurrently by instruction interleaving on the pipeline. Also, the throughput of the DISC can be partitioned in any way between the multiple ISs. Conventional architectures are more concerned with overall performance and throughput than with real-time response. In other words, they optimize the system to the functions that are more heavily used without regard to responsiveness to individual requests. Applications abound where a high degree of responsiveness is required, without too much sacrifice of overall efficiency. This is particularly true in real-time control applications where it is important to optimize the critical loops and respond promptly to interrupts. DISC addresses this problem by dynamically partitioning the processor throughput between multiple instruction streams based upon requirement demands. In this way different tasks and interrupt priorities can be assigned to guarantee their deadlines.
Mycoplasmas and Human prostate cancer: An exciting but cautionary note

A recent study of Barykova, et al. [1] described a significant association between Mycoplasma hominis infection and development of prostate cancer. In the study, the authors detected the presence of M. hominis-specific DNA sequences in examining 496 prostate biopsies by PCR obtained from 248 Russian men undergoing cancer diagnosis. The association appeared to be particularly significant in the statistical analysis between M. hominis infection and development of the higher grade prostate cancer. A possible role for mycoplasmas in association with human malignancy was first noted during 1960s. Several studies reported isolation of mycoplasmas from human leukemic bone marrow [2-6]. A majority of the mycoplasmas isolated in the studies were identified as Mycoplasma fermentans. However, the mycoplasmaoncogenesis hypothesis failed to advance because the same mycoplasmas later could also be found in nonleukemic children or adults, although the mycoplasmas appeared to be most frequently isolated from patients with leukemia [7]. Koch’s postulate of identifying the causative agent in an infectious disease by finding a specific pathogen uniquely present in a particular disease process overshadowed the characteristics in both chronicity and multi-factorial nature of the malignant process. Mycoplasmas are a heterogeneous group of very small organisms capable of self-replication. The wallfree microbes can cause a wide variety of diseases in animals. Some mycoplasmas cause respiratory or urogenital diseases in humans. However, many other mycoplasmas chronically colonize our respiratory and urogenital tracts without apparent clinical significance [8]. Various mechanisms including “antigenic variation” may be critical in the ability of these microbial species to evade host antibody responses or other elements of
A Defect in Glycogen Synthesis Characterizes Insulin Resistance in Hypertensive Patients With Type 2 Diabetes

A subgroup of patients with type 2 diabetes shows a clustering of abnormalities such as peripheral insulin resistance, hypertension, and microalbuminuria. To evaluate whether these traits reflect intrinsic disorders of cell function rather than in vivo environmental effects, we studied a group of 7 nondiabetic hypertensive subjects with an altered albumin excretion rate (AER) (HyMA+) and 3 groups of patients with type 2 diabetes: 7 with normal blood pressure and normal AER (DH−MA−), 7 with high blood pressure and normal AER (DH+MA−), and 7 with both high blood pressure and altered AER (DH+MA+). Glucose disposal was measured during an hyperinsulinemic clamp (40 mU · m2−1 · min−1) with primed deuterated [6.6 2H2] glucose infusion. In the same subjects, a skin biopsy was performed and the following parameters were investigated: glucose transport (as determined by [3H]2-deoxyglucose uptake); glycogen synthase activity (as determined by [14C] glucose incorporation from UDP-[U-14C] glucose into glycogen); glycogen phosphorylase activity (as measured by the incorporation of [U-14C]glucose 1-phosphate into glycogen); and total glycogen content. In vivo glucose disposal was significantly reduced in DH+MA− and DH+MA+, with respect to DH−MA−, HyMA+, and controls. Insulin-stimulated glucose transport was similar in the 3 groups of patients with diabetes. A significant reduction of intracellular glycogen content was observed in DH+MA− and DH+MA+ compared with DH−MA− in both basal and insulin-stimulated conditions, probably because of a major impairment of glycogen synthase activity. Glycogen phosphorylase activity did not show differences between the groups. These results suggest that (1) the combination of type 2 diabetes with hypertension and altered AER is associated with impaired insulin sensitivity, and (2) intrinsic, possibly genetic, factors may account for increased peripheral insulin resistance in hypertensive microalbuminuric patients with type 2 diabetes, pointing to the reduction of glycogen synthase activity as a shared common defect.
An Integrated ISV Call Management Strategy in Heterogeneous Wireless Networks

A lot of wireless standards are proposed to satisfy diversified requirements for mobile users such as IEEE 802.16 and IEEE 802.11. It is feasible to integrate heterogeneous networks to provide complete wireless services. Several strategies were proposed to realize seamless handoff in the heterogeneous networks; however, most of them were only designed to meet system performance or individual QoS requirements for mobile users individually. In this paper, we propose an individual and system views (ISV) strategy integrating the individual view (IV) and system view (SV) to provide the proactive method that can choose the Internet Service Providers by MS and make the deliberated vertical handoff procedures with high throughput of UGS and call management services in heterogeneous networks. Our proposed strategy provides a complete procedure to determine the target network that has not been offered in most papers. Moreover, according to simulation results, the proposed ISV strategy is able to earn significantly lower handoff times than IV and SV and provide stable wireless network given high precedence for UGS traffic and real-time services.
Classwide Peer Tutoring With or Without Competitive Reinforcement: Impact on Academic Growth and Intrinsic Interest

This study examined the effects of Classwide Peer Tutoring on students' academic gains and intrinsic interest in two fourth-grade math classes under two conditions-c-with competitive reinforcement (CWPT + CR) and without competitive reinforcement (CWPT CR). Extending spelling CWPT research of C. C. Cheung and S. Winter (1999), this study utilized an adapted multiplication pretest and posttest and the Attitude Toward Mathematics Scale, developed by Peterson (1978). Study results showed a lack of statistical significance regarding group differences at posttest. However, due to traditional CWPT's impact on classroom atmosphere, peer perception, and learning focus, the investigator recommends eliminating competitive reinforcement for use in a Christian, collaborative classroom. Document Type Thesis Degree Name Master of Education (MEd) Department Graduate Education First Advisor John Van Dyk
The Design and Performance of Real-Time Java Middleware

More than 90 percent of all microprocessors are now used for real-time and embedded applications. The behavior of these applications is often constrained by the physical world. It is therefore important to devise higher-level languages and middleware that meet conventional functional requirements, as well as dependably and productively enforce real-time constraints. We provide two contributions to the study of languages and middleware for real-time and embedded applications. We first describe the architecture of jRate, which is an open-source ahead-of-time-compiled implementation of the RTSJ middleware. We then show performance results obtained using RTJPerf, which is an open-source benchmarking suite that systematically compares the performance of RTSJ middleware implementations. We show that, while research remains to be done to make RTSJ a bullet-proof technology, the initial results are promising. The performance and predictability of JRate provides a baseline for what can be achieved by using ahead-of-time compilation. Likewise, RTJPerf enables researchers and practitioners to evaluate the pros and cons of RTSJ middleware systematically as implementations mature.
Enhanced QoS Mechanisms for IEEE 802.11e Wireless Networks

The quality-of-service (QoS) support for wireless LANs has been a hot research topic during the past few years. In this paper, two QoS provisioning mechanisms are proposed for the employment in 802.11e EDCA MAC scheme. First, the proposed call admission control mechanism can not only guarantee the QoS for the higher priority existing connections but also provide the minimum reserved bandwidth for traffic flows with lower priority. In addition, the adaptive contention window adjustment mechanism can adjust the maximum and minimum contention window size dynamically according to the existing connection number of each AC. The collision probability as well as the packet delay will thus be reduced effectively. Performance results via simulations have revealed the enhanced QoS property achieved by employing these two mechanisms. Keywords—802.11e, admission control, contention window, EDCA
Passive trajectory control of the lateral motion in bipedal walking

This paper proposes passive trajectory control (PTC), a new control method of Acrobot, and discusses its application to biped walking robots. PTC makes the first joint passive and makes the point contact between the whole robot system and the ground, then actuates other joints according to the motion of the passive joint. Due to this interlock, the whole robot system becomes autonomous and the controller is independent of time. Hence, PTC makes it possible to design the robot motion based on not the trajectory of time, but the dynamics around the contact point. In this paper, we design the lateral motion of bipedal walking by means of PTC and realize the dynamic stable motion.
A New Routing Algorithm to Reduce Consumed Energy in Wireless Sensor

Topology control and energy saving is one of the most important problems in wireless sensor networks because of special property of these networks such as limited transmission range, limited power resource and the impossibility of recharging. To solve this problem, CHRA (clustering hierarchical routing algorithm), a centralized cluster formation algorithm for routing algorithm is proposed. At the beginning the centralized algorithm will be used to overcome the defect that the clusters distribute unevenly. After this step, a centralized algorithm will be implemented. The all node sends information about location and energy to the head node in a cluster. after receiving the information, the head node run a dummy center algorithm to select a new head node and a spare head node in the next round. The head nodes run hierarchical based algorithm to create a path through to the sink node. Through network simulation we show that our algorithm reduces average consumed energy and improves network lifetime.